Domestic pig may serve as the most appropriate organ source for human xenotransplantation in the future. However, there is a serious threat of xenogeneic pathogens transmission, especially porcine endogenous retroviruses (PERVs) which are present in genomes of all pigs. The aim of this study was to monitor the prevalence and distribution of PERV DNA in organs of a domestic pig.We used a primer set for a highly conserved fragment of PERV gag sequence to monitor a total PERV DNA copy number and genotype-specific primer sets to study PERV subtypes distribution using Real-Time QPCR (SYBR Green I).Our results showed that PERV DNA was present in all studied pigs, however, most PERV DNA molecules carried numerous mutations thus indicating inability to express functional retroviral particles. The level of PERV DNA in kidney was much higher than in heart (p = 0.007) and in the liver (p = 0.009).It indicates that kidney is potentially the biggest PERV reservoir which makes it the organ of particular concern in xenotransplantation. We also conclude it is possible to monitor pig herds for individuals with the lowest PERV DNA prevalence, especially lacking PERV-C, and perhaps with only defective PERV proviruses that are unable to express functional RNA.