In the cat genome, endogenous feline leukemia virus (enFeLV) exists as multiple, nearly full-length proviral sequences. Even though no infectious virus is produced from enFeLV sequences, transcription and translation have been demonstrated in tissues of healthy cats and in feline cell lines. To test the hypothesis that the enFeLV loads play a role in exogenous FeLV-A infection and pathogenesis, we designed three real-time PCR assays to quantify U3 and env enFeLV loads (two within U3 amplifying different sequences; one within env). Applying these assays, we investigated the loads in blood samples derived from Swiss privately owned domestic cats, specific pathogen-free (SPF) cats and European wildcats (Felis silvestris silvestris). Significant differences in enFeLV loads were observed between privately owned cats and SPF cats as well as among SPF cats originating from different catteries and among domestic cats of different breeds. Within privately owned cats, FeLV-infected cats had higher loads than uninfected cats. In addition, higher enFeLV loads were found in wildcats compared to domestic cats. The assays described herein are important prerequisites to quantify enFeLV loads and thus to investigate the influence of enFeLV loads on the course of FeLV infection.