Objectives Department of Medical Biology, Istanbul Medical Faculty, serves with European Federation of Immunogenetics (EFI) accredited HLA labs for solid organ and bone marrow transplantation facilities both routinely and for research purposes as well as the organization of national and international quality control programs. Design & methods There are 28 HLA tissue typing laboratories in Turkey as of 2008. Department of Medical Biology was determined to be the organizer of ‘National Quality Control Tests for HLA Tissue Typing (NQCT)’ on behalf of Turkish Ministry of Health by the Scientific Committee of Turkish Ministry of Health. NQCT program is performed for the quality assurance of Lymphocyte Cross Match, anti-HLA antibody screening and identification and HLA-A,-B, DR typing by serological and molecular methods. Results and conclusion The first round of NQCT in 2004 included HLA-A,-B typing by serological methods and HLA-DR typing by molecular methods. However, in the following years other tests were also included. The number of participating laboratories was 12 when the program first started and reached 23 by 2008 at the end of fifth round. The discordance rate among the results of the participating laboratories varied from 1.3% to 11.6%. The international quality control program organized by Department of Medical Biology is performed among Balkan Countries, accredited by EFI. This program, which is termed as Balkan External Proficiency Testing (B-EPT), was initiated in 2004 with 11 participants in the first round. The program reached 24 participating laboratories in the fourth round in 2007. This program includes HLA-A,-B,-DR,-DQ tests by molecular and serological methods.