Primary OA is a common multifactorial disease with not fully clarified molecular factors influencing the development of the disease. Among factors disturbing the cartilage integrity are cytokines, such as IL-1, which can stimulate proteinases, resulting in the cartilage destruction. In this regard, IL-1RA competing with IL-1 for binding to its receptor may act as an inhibitor of cartilage breakdown. Because of the possible functional implications, we tested VNTR polymorphism in the second intron of the IL-1RN gene as a putative factor of susceptibility to knee OA. Fifty patients with primary knee OA (diagnosed according to ACR criteria) and 170 healthy controls were included into the study. PCR using primers flanking the VNTR region containing variable numbers of an 86-bp tandem repeat was employed to test the hypothesis. An increased frequency and carriage rate of the IL-1RN*2 allele was found in OA patients in comparison with controls (28 % vs. 15 %, P = 0.0013, OR = 2.97; 95% CI 1.55-5.68 for frequency; 52.5 % vs. 25.3 %, P = 0.0019, OR = 2.95; 95% CI 1.54-5.68 for carriage rate). In addition, a higher frequency of genotype IL-1RN*1/*2 in OA patients was observed as compared with controls (42 % vs. 20.6 %, P = 0.0032, OR = 2.79; 95% CI 1.42-5.48). These results suggest that the IL-1RN*2 allele might represent a factor of susceptibility to OA; however, no correlation between this allele and the markers of cartilage degradation was found.