Porcine endogenous retrovirus C (PERV-C) is a gammaretrovirus present in the genome of many, but not all pigs. PERV-C is an ecotropic virus, able to infect only pig cells. In contrast, PERV-A and PERV-B are present in all pigs, they can infect cells of numerous host species including humans, and therefore pose a risk for xenotransplantation using pigs as donor animals. Intriguingly, PERV-C can recombine with PERV-A and the resulting PERV-A/C recombinants can also infect human cells and replicate to higher titers compared to the paternal PERV-A. Therefore, only PERV-C-free animals should be used for xenotransplantation. When screening wild boars and German landrace pigs for PERV-C, proviral variants were detected, and to detect these variants, new PCR methods were developed. Furthermore, PERVs are known to be active in living pigs as demonstrated by recombination and by different copy numbers in various organs and different parts of an organ. Copy numbers also increased with the age of the animals. This data was obtained by PCR using primers amplifying the highly conserved polymerase sequence which is identical in PERV-A, PERV-B and PERV-C. Here we screened indigenous Greek black pigs, Auckland Island pigs and German slaughterhouse pigs for the presence of PERV-C, using different PCR-based methods and optimized these detection methods. Auckland Island pigs were PERV-C-negative and represent the optimal donor pigs after genetic modifications.