Objective To clone partial env genes of porcine endogenous retrovirus (PERV) isolated from Guangxi Bama minipigs and study their expression differences in different organ tissues.Method The PERV-env genes from peripheral blood leukocytes of Bama minipigs were amplified by RT-PCR, and their homology and phylogenetic analysis were compared with those of some other PERV-env genes published home and abroad. The PERV-env genes obtained by amplification from Bama minipig were used as templates to design primers for analysis on the expressions of PERV mRNA in different tissues of the Bama minipig with a semi-quantitative RT-PCR analysis.Result Differences in the expression levels of PERV mRNA were detected in nine organ tissues of Bama minipig, in which the abundance of PERV mRNA in kidney and peripheral blood lymphocytes was the highest, followed by that in lung, heart, liver, spleen, thymus and ovary, but the expression differences among the six organs were not significant (P>0.05), while the expression abundance of PERV mRNA in pancreas was the lowest.Conclusions The potential risk of PERV infection in using the islet cells of Bama mini pig for xenotransplantation is probably lower than using the other organs. However, further research is still needed.