Non-pathogenic porcine circovirus type 1 (PCV1) and pathogenic PCV2 are widespread in swine herds. In this study, the detection and characterization of PCV1 and PCV2 DNA from porcine-derived commercial pepsin are reported. The complete genomic sequences of the pepsin-derived PCV1 and PCV2 share 76% nucleotide sequence identity with each other and 95-99% identity with respective North American PCV1 and PCV2 isolates. However, the PCV-contaminated pepsin lacks infectivity in PK-15 cells. To further assess the infectivity of the contaminating pepsin in vivo, 16 5-week-old, specific-pathogen-free pigs were divided randomly into three groups: pigs in group 1 (n=5) were each inoculated intramuscularly and intranasally with 4 ml PBS buffer as negative controls, those in group 2 (n=6) were each inoculated with 400 mg contaminated pepsin dissolved in 4 ml PBS and those in group 3 (n=5) were each inoculated with 4 × 10 TCID PCV2 as positive controls. PCV2 viraemia, seroconversion and pathological lesions were detected in group 3 pigs, but not in group 1 or 2 pigs, confirming that the contaminating PCVs were non-infectious. Nevertheless, the detection of PCV DNA in a porcine-derived commercial product raises concern for potential human infection through xenotransplantation.