The RNAs of porcine circovirus type 1 (PCV1) synthesized in PK15 cells were characterized. A total of 12 RNAs were detected. They include the viral capsid protein RNA (CR), a cluster of eight Rep-associated RNAs (designated Rep, Rep', Rep3a, Rep3b, Rep3c-1, Rep3c-2, Rep3c-3, and Rep3c-4), and three NS-associated RNAs (designated NS462, NS642, and NS0). Members of the Rep-associated RNA cluster all share common 5'- and 3'-nucleotide sequences and they share common 3'-nucleotide sequence with the NS-associated RNAs. Rep, capable of coding for the full-length replication-associated protein, appears to be the primary transcript that gives rise to the other seven Rep-associated RNAs by alternate splicing. NS462, NS642, and NS0 appear to have been transcribed from three different promoters present inside ORF1, independent from the Rep promoter. Based on sequence alignment analysis, both the nonpathogenic PCV1 and the pathogenic porcine circovirus type 2 (PCV2) (with nine RNAs: Rep, Rep', Rep3a, Rep3b, Rep3c, NS515, NS672, and NS0) utilize comparable genetic elements similarly located along the genome for viral gene expression. The Rep, Rep', Rep3a, Rep3b, and NS0 of PCV1 and PCV2 are considered equivalent entities in their respective systems. However, quantitative and qualitative differences (splice junction variation) were observed among the Rep3c- and NS-associated RNAs. This work provides a general framework and genetic basis to investigate the biologic properties (and differences) of PCV1 and PCV2.