Abstract Background Efforts to reduce the impact of group A rotaviruses on human morbidity and mortality rely on oral immunisation with live attenuated or recombinant vaccines. A major challenge in immunisation is the vast inter- and intragenotypic diversity accomplished by circulating rotaviruses. Objectives To monitor rotavirus inter- and intragenotypic diversity in hospitalised children. Study design From January 2008 to December 2009 stool samples from 1994 paediatric in-patients suffering from diarrhoea were screened for rotavirus. Rotavirus G- and P-genotypes were determined by nucleotide sequencing and phylogenetic analysis was performed. Results Rotavirus A was detected in stool samples of 341 children, comprising G1P8, G2P4, G3P8, G4P8, G9P8, as well as uncommon G12P6 genotypes and mixed infections. Predominant strains shifted from G1P8 and G9P8 genotypes in the first season to G3P8 and G4P8 genotypes in the second season. The highest intragenotypic diversity was detected in G1 strains and consisted of co-circulating G1-Ic, G1-Id, G1-Ie and G1-II rotaviruses. The G2 analysis revealed different intragenotypic lineages: G2-IIa, G2-IIb and G2-IIc. Interestingly, the circulating G4-Ib rotaviruses were characterised by insertions of 3 or 6 additional coding nucleotides within variable region 4 of VP7. Whereas different G9-III VP7 gene segments were detected G3-Ia sequences were highly homologous. In the VP4 analysis P8-III gene segment predominated over P4-Vb, P8-I, P8-IV and P6-I. Conclusions A remarkable rotavirus heterogeneity was detected in the limited local setting and time span. Continued monitoring and nucleotide sequencing is necessary to document possible effects of rising immunisation levels on intragenotypic rotavirus diversity.