: The human leukocyte antigen (HLA) system (the major histocompatibility system [MHC] in humans) is the main system of tissue tolerance in humans. The genes controlling expression of HLA system molecules are located on chromosome 6 and are divided into 3 classes. Class I is made up of loci: HLA A, HLA B, HLA Cw while class II consists of HLA DR, HLA DQ and HLA DP loci. Main characteristics of this most complex genetic system in humans are extreme gene polymorphism, linkeage disequilibrium, gene segregation, crossing over and population specificity. HLA antigens are one of the most significant factors in solid organ transplantation as well as hematopoieti c stem cell transplantation. Another major importance of HLA system is shown in clinical diagnostics specific HLA alelles are linked to autoimmune disorders, with the greatest association shown between rheumatic (rheumatoid arthritis, psoriatic arthritis , ankylosing spondylitis), gastrointestinal (celiac disease, ulcerative colitis, Crohn's disease) and endocrine diseases (diabetes mellitus, Hashimoto's disease). The aim of this paper was to investigate the association of HLA genes with Crohn's disease an d thereby determine their importance in disease diagnostics and influence on the development of this disease. Chron's disease is a chronic, inflammatory autoimmune bowel disease of unknown etiology which is manifested by a different group of symptoms. Othe r than genetic factors, it is believed that some environmental factors influence the development of the disease together with lifestyle habits and stress. This paper presents a family study of a patient with Crohn's disease and family members where class I and II alelles were determined with PCR SSO (engl. P olymerase C hain R eaction S equence S pecific O ligonucleotides) method. The results of this research showed that the sister suffering from Crohn's disease carries the haplotype HLA C*04, DRB*16, DQA1*01, DQB1*05 inherited from her father. Keywords: