Aims: Investigator-initiated (“academic”) clinical trials (IICTs) are designed and conducted without a participation of any commercial subject. IICTs adopt a patient-oriented approach and attempt to answer relevant questions from the clinical practice. The results obtained by IICTs are considered independent and clinically significant. The purpose of this study was to analyse data from the clinical trial public registers to describe a current status of IICTs and their financial support in the Czech Republic. Methods: The search was performed using four international clinical trials databases - ClinicalTrials.gov, The European Union Clinical Trials Register, BioMed Central ISCTRN (International Standard Randomised Controlled Trial Number) and Australia and New Zealand Clinical Trials Registry (ANZCTR). Entries were filtered by date from 01/01/2004 until 31/01/2017. The terms “Czech Republic”, “Interventional studies“, and “non-commercial” were used. Identified IICTs were categorized by intervention, phase, therapeutic area, design characteristics, and type of funding. Results: In total, 552 trials were identified, from these 40 were recognized as duplicates, and 70 were found having a commercial sponsor, although marked as non-commercial trials, and discarded. Other 39 were discarded because they did not meet the inclusion criteria (the start of the study was beyond the time period or they were only observational). To sum up, the search identified 403 unique IITCs conducting in the Czech Republic. Most of the clinical trials investigated the use of medicinal products and were focused on cancer diseases, followed by cardiovascular diseases. The most common sources of the Czech IITCs’ funding were non 36 profit organizations, including international and national grant agencies, foundations, universities and university hospitals. Conclusion: Despite efforts of the international scientific community, collecting data about clinical trials from the public registers is a time-consuming process, as the registers are incomplete and do not contain transparent information. Currently, only a few multinational randomized IICTs are coordinated by national investigators from the Czech Republic. Considering the importance of IITCs providing more independent and objective results directly applicable in the clinical practice, we hope for an increase of supporting incentives of the government, grant agencies, research institutions, and healthcare providers.