Previous studies have linked levels of porcine endogenous retroviruses (PERV) with poor health and disease in pigs. To determine the levels of expression of PERVs and their potential association with disease expression, real-time reverse transcriptase (RT) PCR assays were used to assess PERV-ABC, PERV-C and PERV-A/C levels in three commercial swine operations in the United States. Pigs (n = 204) aged 3-25 weeks were screened, and all 369 serum samples collected were found to be positive for PERV-ABC RNA as expected. PERV-C and PERV-A/C RNA were detected in 24.1% (89/369) and 18.7% (69/369) of the samples, respectively. When divided into age groups, PERV-A/C RNA was identified in 20.0% (43/215) of the nursery pig samples (3-9 weeks of age) compared to 16.9% (26/154) finisher pig samples (12-25 weeks of age). On two of the farms, serum was collected from healthy pigs (n = 60) and from pen-mates with various clinical conditions including diarrhoea, wasting and respiratory disease (n = 60). Overall, 25% (15/60) of the samples from clinically affected pigs were found to be positive for PERV-A/C RNA, whereas in clinically healthy pigs, only 8.3% (5/60) of the samples were found to be PERV-A/C positive (P = 0.026). It was possible to identify PERV-A/C in the same pigs on more than one consecutive bleeding, indicating variable length of PERV-A/C viremia. The results indicate that there is an increased incidence of PERV-A/C viremia in diseased pigs and that PERV-A/C can be detected over time in selected pigs within commercial pig production systems in the United States.