- Algorithms for Bioinformatics and Computational Genomics
- Applied Security And Privacy (ASAP) Lab
- Automated Program Repair and Tools for Software Maintenance Research Group
- Bilkent Information Retrieval Group
- Bilkent Machine Learning Group
- Bilkent University Multimedia Database Group
- Bilkent University Web Databases Research Group
- BILSEN: Software Engineering and Data Analytics Research Group
- CICEKLAB
- i-Vis Information Visualization Research Lab
- LiRA – Learning for Intelligent Robotic Agents
- Modeling and Visualization Research Group
- Networking and Systems Group
- NeuraVision Research Lab
- Parallel and Distributed Computing Research Group
- P2P Peer-to-Peer Systems Research Group
- RETINA Vision and Learning Group