Background: Gastroenteritis caused by rotavirus is responsible for approximately 810 deaths per year in children under 5 years of age in Peru and emerging rotavirus genotypes have led to concerns regarding cross-protection by the vaccines available. Moreover, there are no reports on the molecular epidemiology of rotavirus diarrhoea in Peru. Methods: A total of 131 stool samples were obtained from children under 5 years hospitalised from January 2010 to December 2012 in the Hospital Regional de Cajamarca (Peru). ELISA and RT-PCR techniques were performed for rotavirus detection. G and P typing of rotavirus-positive samples were performed by semi-nested multiplex RT-PCR, and sequencing was performed to confirm the PCR results. Results: Of the 117 samples available, 22 (18.8%) tested positive for rotavirus by ELISA and 42 (35.9%) tested positive by RT-PCR. Among the G genotypes identified, G9 (35.7%; 15/42) and G12 (33.3%; 14/42) were the most prevalent, with the most common combination being G12/P[6] (23.8%; 10/42). Conclusions: A high prevalence of the G12/P[6] genotype was detected. It is known that this genotype is not covered by the current vaccines available. More in-depth studies are needed to determine the current rotavirus genotypes presents in Peru. © The Author 2014. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved.