- Generation Project Grants
- José Reis Program for the Encouragement of Scientific Journalism
- Research Program on eScience and Data Science
- Scientific Journalism
- Bioenergy Research (BIOEN)
- Improvement in Public Education
- Global Climate Change
- Research in Public Policies
- Biodiversity Research (BIOTA)
- Information Technology and the Development of Advanced Internet (TIDIA) (Program available from 2001 to 2012)
- Integrated System for Hydrometeorology in the State of São Paulo (SIHESP)
- Inter-institutional Cooperation to Support Brain Research (CINAPCE)
- Structural Biology Network on Advanced Topics in Life Sciences (Smolbnet)
- Genomics
- Viral Genetic Diversity Network (VGDN) (Program available from 2000 to 2005)