- Agricultural Microbiology
- Agricultural Engineering Systems
- Animal Science and Pastures
- Applied Ecology (inter-unit: USP/ESALQ and CENA)
- Applied Economics
- Bioenergy (inter-institutional: USP, Unicamp and Unesp)
- Bioinformatics (inter-unit: USP/ESALQ and IME)
- Crop Science
- Entomology
- Food Science and Technology
- Forest Resources
- Genetics and Plant Breeding
- International Cellular and Molecular Plant Biology (Ph.D.) (international: USP/ESALQ, OSU and Rutgers)
- Plant Pathology
- Plant Physiology and Biochemistry
- Soil and Plant Nutrition
- Statistics and Agricultural Experimentation
