Genotypes of porcine circovirus type 2 (PCV2) in clinical tissue specimens collected from pigs of different region in China between 2001 and 2003 were analyzed by PCR and restriction fragment length polymorphism (RFLP) analysis of PCV2 genomic DNA encompassing the complete ORF2. The results showed that nine different genotypes (A-I) were identified and designated CHN-2A, CHN-2B, CHN-2C, CHN-2D, CHN-2E, CHN-2F, CHN-2G, CHN-2H and CHN-2I, respectively. Amongst the genotypes, 0.6% were CHN-2A (1/173), CHN-2B (1/173) and CHN-2C (1/173) RFLP profile; 2.3% were CHN-2F (4/173) and CHN-2G (4/173); 5.8% were CHN-2D (10/173); 8.6% were CHN-2E (15/173); 18.5% were CHN-2I (32/173) and 60.7% were CHN-2H (105/173). Therefore, our results suggest that CHN-2H is the dominant genotype of PCV2 prevailing in China. Sequence analysis revealed that ORF2 genes of different genotypic PCV2 exhibited the variation extent of 90.5-99.5% and 88-100% in nucleotide and amino acid respectively. The deduced amino acid sequences alignment of the capsid protein encoded by ORF2 of PCV2 presented that three major regions with greater heterogeneity existed at residues 57-90, 121-136 and 180-191 among nine genotypic PCV2. It was concluded that there exist variation in ORF2 genes of different genotypic PCV2 prevailing in China.