This department is responsible to manage the reproduction and breeding of animals using the most appropriate and acceptable breeding technologies and techniques.

The core departmental functions are;

1. Conservation of the indigenous Animal Genetic Resources in Uganda
2. Establishing of Breeding Structures in the country (e.g. Open Nucleus Breeding, Breeder Associations/Societies, Satellite Centres) for Genetic improvement
3. Adaptation and Application of Breeding & Production technologies (e.g. Assisted Reproductive Technologies.
4. Sensitization & Specialized Training of Technicians and other Stakeholders.
5. Selection of Superior Dams and Sires produced on Centre farms.
6. Collaboration in Breeding Research with other Stakeholders.

Some of the specialised units under Breeding and reproduction includes;

1. Conservation and Gene banking (National & Eastern African Regional)
2. Foundation fish brooder stock & fry production Unit
3. National Small Ruminants Breeding Resources Centre unit
4. National Pig Grand-parent Resources Centre Unit
5. Community-based Breeding Program –AI, MOET, In-Vitro Fertilization (IVF), Genomic EBV estimation through Satellite Centre