Kashin-Beck disease (KBD) is an endemic and deformable osteoarthrosis. Epidemiological study has revealed that lower Se level is the principal environmental factor in the pathogenesis of KBD. Selenoprotein P (SEPP1) is a special selenoprotein, which is the primary form of Se in vivo. Our aim was to investigate the putative association of SEPP1 r25191g/a single nucleotide polymorphism (SNP) with KBD risk and the SEPP1 transcriptional levels in whole blood and articular cartilage tissue of KBD cases and controls, respectively. One hundred and sixty-seven cases with KBD and 166 control subjects from Shaanxi province of China were included in the present study. The detection of SNP r25191g/a in the 3' untranslated region was performed using an efficient technique, tetra-primer amplification refractory mutation system PCR. A quantitative analysis of SEPP1 mRNA in KBD and control groups by real-time PCR was also performed. The present results show no significant difference in genotype and allele distribution of SNP r25191g/a between individuals with KBD and controls (P = 0·279 and 0·428, respectively). There was also no association between SNP r25191g/a and risk of KBD (OR 1·153; 95 % CI 0·533, 2·496). However, the frequency of the rare genotype AG of SNP r25191g/a was significantly lower in Chinese population than in the Caucasians. It was shown that the SEPP1 mRNA expression in whole blood was lower in KBD patients than in the control group (0·149-fold, P < 0·001), but that it was much higher in articular cartilage tissue (4·53-fold, P = 0·012). Our aim was to lay a foundation for us to further study the association between the pathogenesis of KBD and SEPP1.