- the state decoration Order of the White Star 3rd class was awarded to Professor Jaak Vilo
- UT decoration of honour - Tiina Lasn.
UT decoration of honour - Heiki-Jaan Kaalep.
EMT-Elion scholarship - Tauno Metsalu and Tiina Turban.
UT decoration of honour - Ülle Holm.
- Lecturer of the year - Eno Tõnisson
- Researcher of the year - Satish Srirama
- Positive person of the year - Laura Kalda
- Accomplisher of the year - Margus Niitsoo
Best young scientist award from the president of Estonia professor Peeter Laud.
- Main prize Leopold Parts (Wellcome Trust Sanger Institute and Cambridge University, previously student of computer science at Tartu Unviversity, member of BIIT research group),
- II prize Meelis Kull (supervisor Jaak Vilo), Statistical enrichment analysis in algorithms for studying gene regulation.
- III prize Margus Niitsoo (supervisor Ahto Buldas), Black-box Oracle Separation Techniques with Applications in Time-stamping.
University of Tartu and Society of Mathematics of Estonia: Eno Tõnisson - for mathematics education.
MODELS'2011 Ten-Year Most Influential Paper Award - Marlon Dumas
Ministry of Science and Education:
- Main prize - Jüri Reimandi (supervisor Jaak Vilo) Functional analysis of gene lists, networks and regulatory systems (doctoral theses)
- I prize - Kaur Alasoo (supervisors: Hedi Peterson and Phaedra Agius), Combining Support Vector Machines to Predict Novel Angiogenesis Genes (in bachelor theses)
Estonian Academy of Sciences, Best Bachelors Thesis Award - Kaur Alasoo (supervisors: Hedi Peterson and Phaedra Agius) for "Combining Support Vector Machines to Predict Novel Angiogenesis Genes"
IWSEC'2010 Best Paper Award - Margus Niitsoo, "Optimal Adversary Behavior for the Serial Model of Financial Attack Trees"
BPM'2010 Best Paper Award - Luciano García-Bañuelos and Marlon Dumas, "Structuring Acyclic Process Models"