The objective of this study was to investigate, by partial sequencing of VP2 protein, the variability of CPV detected in 37 fecal samples collected from vaccinated puppies with enteritis. Laboratorial diagnosis of CPV was confirmed by HA/HI and PCR and, for sequencing analyses, two different regions of the VP2 gene were amplified by PCR. From 1995 to 2004, all strains were characterized as CPV-2a. After that, both CPV-2a and CPV-2b were detected. All CPV-2a showed a non-synonymous mutation in the residue 297 (Ser→Ala). A synonymous substitution at the AA 574 was also observed in 15/37 samples. Our findings indicate that the cases of vaccine failure are most likely not associated to the mutations detected in the sequenced regions. However, the monitoring of genotyping mutations that led to new CPV strains is essential to determinate if current vaccines will keep providing protection against all new future variants.