Genetic factors have been implicated in the pathogenesis of osteoporosis, a common disorder in primary biliary cirrhosis. Oestrogen receptor-alpha gene, vitamin D receptor gene and interleukin-1 receptor antagonist gene are all attractive candidates for osteoporosis susceptibility. We investigated the polymorphisms of the above genes and bone disease in Hungarian patients with primary biliary cirrhosis.Thirty-three female patients with primary biliary cirrhosis were enrolled (age range, 39-72 years; anti-mitochondrial antibody M2 positive, stage II-IV). Eighty-four healthy and 76 osteoporotic age matched female subjects served as controls. Vitamin D receptor BsmI, interleukin-1 receptor antagonist gene variable- number tandem repeat and oestrogen receptor-alpha PvuII and XbaI polymorphisms were determined. Bone mineral density was measured by dual energy X-ray absorptiometry (XR26, Norland) in lumbar spine and femoral neck.The genotype frequency of vitamin D receptor BsmI (BB, 57.5%; Bb, 33.3%; bb, 9.1%) and oestrogen receptor-alpha PvuII (PP, 18.2%; Pp, 75.6%; pp, 6.2%) and XbaI (XX, 9.1%; Xx, 90.9%; xx, 0%) of the primary biliary cirrhosis patients was different from that of the healthy and osteoporotic control groups (P < 0.03 for each). Osteoporosis (t score < -2.5) was present in 42.4% of the patients. Osteoporotic primary biliary cirrhosis patients were older and had a longer disease history (P = 0.01 for both). No association was found between the polymorphisms and bone mineral density values at either position.We confirmed previous findings concerning the higher frequency of vitamin D receptor BsmI BB genotype in patients with primary biliary cirrhosis. The oestrogen receptor-alpha PvuII and XbaI Pp and Xx genotypes were more frequent in primary biliary cirrhosis patients, while interleukin-1 receptor antagonist gene variable-number tandem repeat polymorphism was not different. Since none of the polymorphisms was associated with bone mineral density, it is unlikely that these polymorphisms are essential in predicting bone mineral density in primary biliary cirrhosis.