This investigation describes the molecular characterization of P[6]G2 rotavirus strains from hospitalized neonates with community-acquired diarrhea (CAD), nosocomial diarrhea (ND), and asymptomatic nosocomial infection (ANI) in Belém, Brazil. Twenty-six rotavirus strains with P[6]G2 genotype were sequenced to genes coding for VP4, VP7, and NSP4 proteins. Phylogenetic analysis of the VP4 gene, including prototype strains RV3, ST3, M37, and U1205, showed that local P[6]G2 strains clustered forming a distinct lineage (bootstrap of 99%). Brazilian P[6]G2 strains had the highest homology (ranging from 96.0%-98.3%) with the African strain GR1107, G4P[6]. Phylogenetic tree for VP7 gene was constructed including old and new G2 African strains SA3958GR/97, SA356PT/96, SA514GR/87, SA4476PT/97, BF3676/99, GH1803/99, and representative strains of G1, G3, G4, G5, G8, and G9 genotypes. The Brazilian P[6]G2 samples fell into a distinct group (bootstrap value of 97%) and showed homology rates ranging from 92.1% to 93.5% with P[6]G2 African strains BF3676/99, GH1803/99, and SA3958GR/97. Nucleotide sequence analysis of the NSP4 gene, including human prototype strains S2, KUN, DS-1, RV5, RV3 and ST3, and animal prototype OSU, showed that all neonatal isolates fell into genotype A and clustered with a bootstrap value of 100%, with in-group similarities ranging from 99.3% to 100%. In this study no significant differences in nucleotide sequences of the VP4, VP7, and NSP4 genes could be observed when comparing diarrheic (CAD and ND) and non-diarrheic (ANI) babies. Monitoring of rotavirus strains in hospital environments is of particular importance, since it is claimed currently that an efficacious rotavirus vaccine, when available for routine use, will determine an impact on hospital-acquired rotavirus disease.