Author: PD Dr. Ghazaleh Gouya-Lechner, Founder, Gouya Insights | Last reviewed: May 2026
From 31 January 2025, every new clinical trial in the European Union and European Economic Area must be submitted, managed, and tracked through a single digital platform: the Clinical Trials Information System, known as CTIS. If you are a founder or clinical lead at an early-stage biotech company planning your first EU trial, CTIS is the mandatory entry point for your application, your ongoing communications with regulators, and your trial’s public record. There is no alternative national route for trials initiated from that date forward.
This article covers what CTIS is, how a submission is structured, what the 2024 transparency rules mean for your dossier, country-specific opportunities within the system, the most common submission pitfalls, how secondary use of samples and post-trial access are handled, and practical resources for getting started.
CTIS is the EU-wide platform that replaced 27 separate national submission systems with one. Created under Regulation (EU) No 536/2014, also known as the Clinical Trials Regulation or CTR, it was built to solve a straightforward problem: before CTIS, a sponsor running a trial in Austria, Germany, and France simultaneously had to manage three parallel submissions, three sets of national documents, and three independent review processes. One application now covers all of it.
From a regulatory standpoint, CTIS serves four main functions.
A CTIS submission is divided into two parts, assessed by different bodies on different timelines, both of which must be approved before a trial can begin.
Part I covers everything related to the investigational medicinal product and the scientific basis of the trial. This includes the Investigator’s Brochure (IB), the Investigational Medicinal Product Dossier (IMPD), the clinical trial protocol, and the scientific rationale for the study. Part I is assessed collaboratively: one member state takes the lead as the Reporting Member State, and the other participating countries review and comment in parallel. The outcome of the Part I assessment applies consistently across all participating member states.
Part II covers the national and site-specific elements: ethics committee review, patient-facing documents including the informed consent form, and any country-specific requirements related to local regulations, privacy law, or reimbursement.
Both parts must be fully approved before any trial site can be initiated. They can be submitted simultaneously or in sequence, but managing both clocks at once is one of the most common operational gaps in first CTIS submissions. Sponsors need to assign roles within the platform, plan their redaction strategy, and track Part I and Part II timelines in parallel from the start, since delays in either stream affect the overall timeline
Since 18 June 2024, most information about an authorised trial becomes public through the CTIS portal [1]. This includes the protocol, the scientific basis of the trial, the results summary, and the lay summary written for patients. Sponsors who are accustomed to treating trial protocols as confidential documents need to adjust their approach before submitting to CTIS.
Commercially confidential information (CCI) and personal data can be protected, but only with a documented justification submitted as part of the application. This is not automatic. Sponsors must proactively identify which elements of their dossier qualify and prepare a redaction justification that distinguishes genuine CCI from general scientific information, which does not qualify.
Teams that approach this at the last minute frequently discover that their justifications are insufficient or that they have not drawn the right boundaries between what is and is not protectable. Your redaction strategy should be part of your CTIS preparation, not something assembled after authorisation. Align your legal, regulatory, and clinical teams on this before submission.
Austria, Belgium, and Germany have all committed to review timelines less than a third of the EU-wide average . Dossiers take approximately 35 days, while the EU-wide average sits at around 110 days.
This matters most for first-in-human studies, where sponsors may choose a single country to start before expanding to a multi-country program. Austria, with its regulatory infrastructure at AGES (the Austrian Agency for Health and Food Safety) and its experienced ethics committees, is a practical choice for early-phase submissions. Pre-submission dialogue with AGES is accessible and can help sponsors identify gaps in their dossier before the formal clock starts.
The 35-day timeline is conditional on submission quality. Applications with deficiencies in the IMPD, the protocol, or the national documents will not benefit from faster review. The investment in preparation is what unlocks the timeline advantage.
Across the submissions we have supported, there are a set of problems that account for the majority of delays and regulatory questions. Understanding these in advance is one of the most practical things a sponsor can do before preparing their CTIS application.
IMPD quality deficiencies are the most frequent source of questions during Part I review. Recurring problems include missing or outdated stability data, insufficient comparability justification following manufacturing changes, and inadequate discussion of how non-clinical findings translate to human risk. An IMPD that presents preclinical data without contextualising what it means for human dose selection, safety monitoring, or patient eligibility will attract regulatory questions that trigger clock stops.
Investigator’s Brochure weaknesses often relate to how non-clinical data is framed. Reviewers expect the IB to explain what non-clinical findings imply for human risk, what safety signals to monitor, and where the preclinical models have limitations. An IB that reads as a summary of experiments rather than a clinical risk document is a common problem, particularly for sponsors who have drafted their own without regulatory writing support.
While Part I assessment is consistent across all countries, Part II is deliberately left national. Each member state retains the right to apply its own legal requirements for ethics review, informed consent, data protection, and patient rights. CTIS did not change that.
Part II document quality is a consistent source of delays at the national level. The most frequent issues are informed consent forms that are too generic or not adapted to country-specific requirements, documents that are too long, and translations that are technically accurate but not readable for patients. Poorly prepared consent forms create revision cycles that delay site initiation.
Operational planning gaps are common in first submissions and entirely preventable. These include failing to assign system roles before the submission window opens, underestimating the time required to prepare a redaction strategy, and not tracking the Part I and Part II timelines simultaneously. The platform has a learning curve, and the operational overhead of a first CTIS submission is consistently higher than sponsors expect.
Two elements that sponsors overlook are secondary use of biological samples and post-trial access arrangements, both of which must be addressed in Part II and both of which are country-specific.
Secondary use of samples refers to whether biological samples collected during the trial can be used for purposes beyond the primary research question, such as biomarker research or future studies. Each member state has its own legal and ethical framework for this, and the informed consent form must reflect the specific permissions being requested in that country.
Post-trial access refers to whether and how patients can continue to access the investigational treatment after the trial has ended. This is relevant in early-phase trials where patients may have responded to treatment and have no alternative options. The arrangements need to be specified in the protocol and the patient-facing documents, and they need to be realistic given the regulatory and commercial status of the product at the time the trial closes.
Sponsors who address these points with boilerplate language copied from a previous trial in a different country often receive ethics committee questions that add weeks to the Part II review.
| Resource | What It Covers | Where to Find It |
|---|---|---|
| EMA CTIS Sponsor Handbook (March 2026) | Primary operational guide: role management, submission workflows, publication settings, deadline tracking | Download Sponsor Handbook (PDF) |
| EMA Sponsor FAQ | Current questions on CTIS functionality, CTR interpretation, and country-specific submission points. Updated regularly. | Download FAQ Document (PDF) |
| EMA Walk-in Clinics and Bitesize Talks | Training and support page listing all upcoming live sessions where sponsors can ask operational questions directly to EMA staff. | EMA Training & Support Page |
| EMA CTIS Service Desk | Support for platform access issues, technical errors, and submission system questions | EMA Contacts Directory |
| EudraLex Volume 10 | The full clinical trials regulatory framework: CTR text, guidance documents, Q&A, and national contact points for each member state | EudraLex Volume 10 Hub |
| National Contact Points | Country-specific requirements for Part II documents, ethics review, and consent form content — listed in Annex III of the Q&A document | Download Annex III Q&A (PDF) |
The problems sponsors encounter at submission time are usually created during preclinical development, when no one is yet asking the clinical questions.
One company came to us to develop the clinical study protocol for a topical drug for chronic wounds. They were ready to enter the clinical stage. When we reviewed the development package, two gaps became visible immediately. The first was formulation: the drug had been developed as a solution, but a solution applied to an open wound does not stay in place. The appropriate formulation was a gel or cream, but switching formulation requires demonstrating that the molecule retains its properties in the new form and releases appropriately. That data did not exist. The second gap was treatment duration: chronic wounds require a minimum of four weeks of treatment to generate meaningful clinical data, but the company’s toxicology studies covered only one week of exposure. Both gaps required new experiments before the trial could proceed.
Both problems had the same root cause. The team had moved through preclinical development without asking what a clinical trial in this indication would actually require. If those questions had been part of the development plan from the start, the formulation program and toxicology package would have been designed accordingly.
This is one of the most common patterns we see. CTIS does not create these problems, but it makes them visible at the point where they are most costly to fix. The investment in early regulatory planning is what determines whether a submission moves cleanly through review or triggers a cascade of questions and clock stops.
What does CTIS stand for and what is it used for? CTIS stands for Clinical Trials Information System. It is the EU-wide platform for submitting clinical trial applications, managing the trial lifecycle, and publishing trial information under Regulation (EU) No 536/2014. Every sponsor planning a clinical trial in the EU or EEA must use it.
Do I have to use CTIS for my clinical trial in Europe? Yes. Since 31 January 2025, all new clinical trial applications in the EU and EEA must go through CTIS. There is no national submission alternative for trials initiated from that date.
How long does it take to get a clinical trial approved in Europe through CTIS? It depends on the member state and the quality of the dossier. Austria, Belgium, and Germany have committed to approximately 35 days for well-prepared applications, less than a third of the EU-wide average of around 110 days. The 110-day figure reflects real calendar time from submission to decision, which includes clock stops for information requests and validation periods that the regulation does not count against the official timeline. Dossiers with deficiencies trigger additional clock stops and can extend the process further.
What is the difference between Part I and Part II in CTIS? Part I covers the scientific and product-level content of the application and is assessed in a coordinated way across all participating member states. Part II covers national and site-specific elements, including ethics review and patient-facing documents, and is assessed independently by each member state. CTIS harmonised the submission process and the Part I assessment, but Part II remains national. Each member state retains its own legal requirements for ethics review, informed consent, and data protection, which the CTR did not standardise.
What information about my clinical trial will become public through CTIS? Since 18 June 2024, once a trial is authorised, most core information becomes publicly available through the CTIS portal, including the protocol and results summaries. Commercially confidential information and personal data can be protected, but only with a documented justification submitted as part of the application. This is not automatic and must be planned before submission.
Can I start a clinical trial in just one EU country through CTIS? Yes. CTIS supports both mono-national and multi-country applications. For early-phase trials, starting in a single country such as Austria is a common and practical approach that allows sponsors to move faster before expanding.
What is an IMPD and why does it keep getting flagged in regulatory review? The Investigational Medicinal Product Dossier (IMPD) describes the quality, manufacture, and non-clinical data for the investigational product. It is the most frequently questioned section in Part I review because it requires not just data but a clinical interpretation of what that data means for human use. Sponsors often present preclinical results without contextualising them for dose selection, safety monitoring, or patient eligibility, which triggers regulatory questions.
How early should we start preparing a CTIS submission? For a first submission, preparation should begin at least three to six months before the target submission date. This allows time to resolve IMPD gaps, prepare national documents, develop a redaction strategy, assign platform roles, and align the clinical and regulatory team before the formal clock starts.
Why do informed consent forms still need to be adapted per country if CTIS harmonised the process? CTIS harmonised the submission platform and the Part I scientific assessment, but Part II remains national. Informed consent forms must reflect the legal requirements of each member state, including national data protection rules and language expectations, which the CTR did not standardise. The same applies to secondary use of samples and post-trial access, both of which are governed by national bioethics and data protection law.
When did CTIS become mandatory for EU clinical trials? CTIS became mandatory on 31 January 2025. From that date, all new clinical trial applications in the EU and EEA must go through CTIS. There is no national submission alternative for trials initiated from that date.
References
[1] European Medicines Agency. Clinical Trials Regulation (EU) No 536/2014 and CTIS transparency rules applicable from 18 June 2024. https://www.ema.europa.eu/en/human-regulatory-overview/research-development/clinical-trials-regulation
[2] European Commission and Member States. Joint Recommendations on Recurrent Submission Deficiencies in CTIS Applications. EudraLex Volume 10. https://health.ec.europa.eu/medicinal-products/eudralex/eudralex-volume-10_en
[3] Pharma Intelligence. Clinical Trial Approvals in EU: Pharma Pushes for 60-Day Standard as CTR Delays Persist. September 2025. https://insights.citeline.com/pink-sheet/r-and-d/clinical-trials/clinical-trial-approvals-in-eu-pharma-pushes-for-60-day-standard-as-ctr-delays-persist-CY6FBHYTVNGCHN6RQDSQ3RFCLY
[4] European Medicines Agency. CTIS Sponsor Handbook (March 2026). https://www.ema.europa.eu/en/documents/other/clinical-trial-information-system-ctis-sponsor-handbook_en.pdf
[5] European Medicines Agency. CTIS Sponsor Frequently Asked Questions (March 2026). https://www.ema.europa.eu/en/documents/presentation/clinical-trial-information-system-ctis-frequently-asked-questions_en.pdf
[6] European Medicines Agency. CTIS Training and Support — Walk-in Clinics, Bitesize Talks, and Sponsor Resources. https://www.ema.europa.eu/en/human-regulatory-overview/research-development/clinical-trials-human-medicines/clinical-trials-information-system-ctis-training-support
About the Author
PD Dr. Ghazaleh Gouya-Lechner is the founder of Gouya Insights and a cardiologist with over 20 years of hands-on clinical practice. She has worked across clinical development, regulatory strategy, and pharmacovigilance for both pharmaceutical and medical device companies. In 2017 she founded Gouya Insights, a CRO supporting early-stage biotech and medtech companies through clinical trials and drug development.
Nora holds degrees in law from Janus Pannonius University and in pharmacy from Semmelweis University, combining legal and scientific expertise. She is a certified Data Protection Officer with hands-on experience supporting GDPR compliance and contractual safeguards for biotech and pharma clients. With over 20 years in clinical research, she brings a pragmatic, risk-aware approach to data protection in global trials
