Objective: This report presents an overview on the progress of clinical trials in Indonesia based on database assessment from clinical trial registries.Methods: Study records that were registered up to December 26, 2018, were extracted from three clinical trial registries (ClinicalTrials.gov, ISRCTN registry, and EudraCT) and a clinical trial register (WHO Intational Clinical Trials Registry Platform (ICTRP)) with the keyword Indonesia. A total of 505 records comprised of 402 interventional studies and 103 observational studies were found and analyzed. Results: The top five noncommunicable diseases (NCDs) studied were cancers, diabetes, cardiac diseases, hypertension, and gastrointestinal diseases, while the top five infectious diseases (IDs) were malaria, tuberculosis, vaccines for IDs, HIV, and dengue. Remarkably, the proportion of regional studies (within Indonesia only) was higher than that of multiregional studies (including areas outside of Indonesia) in general. This trend became most apparent after the issuance of national regulations on Material Transfer Agreements (MTA) and other rules. Upon closer scrutiny, regional clinical trials and multiregional clinical trials (MRCTs) in Indonesia differed in terms of sponsorship, target population and size, interventions, and study phases. Conclusions: The total number of clinical trials in Indonesia is increasing and is mainly attributed to the growing number of regional clinical trials sponsored from within the country. Interrelated factors have shaped the characteristics of these as compared to the dwindling number of MRCTs. Establishment of a national level of management is an option that can better facilitate both MRCTs as well as regional clinical trials, to better address the national health issues, and to cope with the regulations.