Xenotransplantation of porcine organs has the potential to overcome the acute shortage of human tissues and organs for human transplantation. Swine represents an ideal source of such organs owing to their anatomical and physiological similarities to human besides their plentiful supply. However, this procedure is also associated with a number of safety issues related to zoonotic infections. Among such zoonotically important pathogens, porcine endogenous viruses (PERVs) represent the most concerned virus as they persist asymptomatically and show germline transmission in pigs. They belong to gamma retroviruses and are of three types viruses: A, B and C. In the present study, PCR based cloning was performed with chromosomal DNA extracted from miniature pigs to analyze the envelope gene of PERVs. Amplified PCR fragments of about 1.5 Kb, covering the partial env gene, were cloned into pCR2.1-TOPO vectors and sequenced. A total of 51 env clones were obtained from two miniature pigs, types M149 and T1111 Phylogenetic analysis of these genes revealed the presence of only PERV type A and B in the proportion of 45% and 55%, respectively. Among these, 9 clones had the correct open reading frame: eight were PERV type A and one PERV type B. Since both these PERV types are polytropic and have the capacity to infect human cells, our data raise a concern that proviral PERVs might have the potential to generate infectious viruses during or after xenotransplantation in humans.