Background: Clinical trials provide one of the highest level of evidence to support medical practice. Investigator initiated clinical trials (IICTs) answer relevant questions in clinical practice that may not be addressed by industry. This study aims to compare, for the first time, two European Countries in terms of registered IICTs, respective funders, scientific outcome and its impact on the national performance in IICTs. Methods: A retrospective systematic search of registered IICTs, over the past 13 years, using four clinical trials registries was carried out in two European countries with similar population and Gross Domestic Product (GDP) but with different governmental models to fund clinical research. Each completed IICT was screened for sponsors, funders, type of intervention and associated publications. Results: IICTs involving Czech Republic and Portugal were n=439 (42 % with hospitals as sponsors) and n=328 (47 % with universities as sponsors), respectively. Funding agencies (national and international) supported only 25 % and 18 % of the IICTs in Czech Republic and Portugal, respectively. The Czech Ministry of Health, through the Health Research Council, supported 61 IICTs and the Portuguese Ministry of Science, Technology and High Education, through Fundação para a Ciência e Tecnologia , supported 27 IICTs. Among these, trials with investigational medicinal products represent 52 % (n= 32/61) and 4 % (n=1/27) in Czech Republic and Portugal, respectively. The Czech Republic presented a higher percentage of IICTs´ publications in high impact factor journals (IF>21) with national investigators as authors, when compared to Portugal (86 % vs 15 %). Conclusion: We found a better performance of Czech Republic in terms of number and scientific outcome of IICTs when compared to Portugal. These findings might be related to the existence of specific and periodic funding for clinical research in Czech Republic, although further data still need to be collected to confirm this relationship.