A rotavirus surveillance study was undertaken in Slovenia from December 2005 to March 2006. Stool samples from 114 children hospitalized with acute viral gastroenteritis were collected from two main Slovenian hospitals. These confirmed rotavirus-positive samples were selected for a rotavirus G and P genotype prevalence study. Six untypable strains of genotype G were further analyzed with sequencing of the VP7, VP8*, and NSP4 genes. The findings of the study were that the G1 genotype was the most prevalent, found in 72 samples (63.2%), followed by G9 in 26 samples (22.8%), G4 in 10 samples (8.8%), and G3 in 2 samples (1.7%). All G genotypes were combined with the P[8] genotype specificity. After sequence analysis, one G8 and two G12 genotypes were also characterized. In a VP7-based phylogenetic analysis, the G8P[8] strain (SI-885/06) was more closely related to the Cody I801 bovine strain than to other human strains. Both G12 strains (SI-264/06 and SI-403/06) were shown to belong to the Se585 G12 cluster. In the VP8* phylogenetic tree, all analyzed strains except one, belonged to the P[8] lineage II and shared high identity in amino acid sequence. All characterized strains were clustered into the NSP4 genotype B. The molecular characterization of this G8 strain supports the theory of interspecies transmission of rotaviruses and animal-human genome reassortment. This is the first report on rotavirus G12 detection in Slovenia.