ABSTRACT Pigs have been utilized as the donor animal for xenotransplantation, a promising solution to the continued shortage of organ donor. However, porcine endogenous retrovirus (PERV), a gamma retrovirus present in all pig genomes, remains a major concern for the microbiological safety of donor pigs. Therefore, accurately assessing the risk of PERV infection is essential for the clinical application of xenotransplantation. To improve the evaluation of PERV infectivity, here we developed a new in vitro co‐culture method for porcine and human cells, applying flowcytometric cell sorter for specific isolation of human cells. This method allows direct contact between porcine and human cells without special treatment that would affect PERV replication, which is better simulating the situation observed in in vivo xenotransplantation. Using this method, we identified several possible factors affecting PERV infectivity, including the period during which porcine and human cells are in contact, the number of porcine cells used, and the levels of PERV mRNA expression in porcine cells. Notably, we found that the PERV infection of human cells can occur within the first 24 h of contact if porcine cells are of a high‐risk type for PERV infection, which is not confirmed by any types of conventional co‐culture methods. Our result emphasized the importance of selecting appropriate donor pigs with lower risk of PERV infection. Our newly developed method may help the testing and selection of pigs with lower risk of PERV infection.