<p class="abstract"><strong>Background:</strong> A low rate of investment in science it is directly impacts the technological independence and capacity in health care costs. Knowledge of funding sources is critical to understand the problem and formulates hypotheses for future studies.</p><p class="abstract"><strong>Methods:</strong> Two databases were used: the System for Control of Clinical Research (SCCR) from the Brazilian Health Surveillance Agency (Anvisa), and the International Clinical Trials Registry Platform (ICTRP). </p><p class="abstract"><strong>Results:</strong> From 2009 to 2012, 77% of the clinical trials approved by Anvisa were sponsored by transnational pharmaceutical industry. On the other hand, the national pharmaceutical industry sponsored 8% of the trials over the same period. The most frequent sponsor of clinical trials involving drugs registered in the ICTRP from 2011 to 2012 was the transnational pharmaceutical industry (43%). Among the trials with national sponsors, are those involving neglected diseases such as chronic hepatitis C (ICD X B18.2), cutaneous leishmaniasis (ICD X B55.1) and yellow fever (ICD X A95), which were all sponsored by national governmental foundations. None of the active pharmaceutical ingredients studied by the transnational pharmaceutical industry or the transnational biopharmaceutical company were in the national list of essential medicines. On the other hand, 83% and 66.6% of the active pharmaceutical ingredients studied by national private universities and the international governmental agency, respectively, are in the national list of essential medicines. </p><p class="abstract"><strong>Conclusions:</strong> The national pharmaceutical industry and government still invests little in Research and Development (R&D) activities, when compared with transnational industries. This affects directly its technological and innovation ability.</p>