- Accelerated Network Technologies Research Group (ANT)
- AeroWorks (AeroWorks)
- Automata@FIT (Automata@FIT)
- Automated Analysis and Verification Research Group - VeriFIT (VERIFIT)
- Cognitive and Neural Engineering Research group (CANE)
- Computational Photography Group - CPhoto@FIT (CPHOTO)
- Computer Graphics Research Group (GRAPH)
- Dependable Digital Systems Research Group (DEPSYS)
- Evolvable Hardware Research Group (EHW)
- Formal Model Research Group (FM)
- High Performance Computing Research Group (HPC)
- IT Security Research Group (Security@FIT)
- Information and Database Systems Research Group (IS)
- Intelligent Systems Research Group (INTSYS)
- Knowledge Technology Research Group (KNOT)
- Management of software engineering Research Group (MSWI)
- NES@FIT - Networks and distributed systems research group (NES@FIT)
- Robotic research group Robo@FIT (ROBO)
- Security Technology Research and Development (STRaDe)
- Speech Data Mining Research Group BUT Speech@FIT (SPEECH)
- Supercomputing Technologies Research Group SC@FIT (SC@FIT)