Despite the high incidence of rotavirus gastroenteritis, secondary bacteraemia later in the course of the disease has rarely been reported. To date, the exact incidence of this complication has not been determined. A prospective study was conducted between January 2007 and December 2008 to determine the incidence of bacteraemia by organisms of the normal intestinal flora during severe rotavirus gastroenteritis. Rotavirus gastroenteritis was diagnosed by antigen detection in stool. A previously described 20-point numerical score system was used to determine the severity of disease. There were 289 cases (30%) of rotavirus gastroenteritis during the study period, 106 (36.7%) of which were accepted to be severe rotavirus gastroenteritis and hospitalized. On admission stool and blood cultures tested negative. In cases of persistent or recurrent fever, additional blood cultures were obtained. Among cases with severe rotavirus gastroenteritis, 4 (3.8%) had positive blood cultures (Klebsiella pneumoniae in 1 patient, Escherichia coli in 1 patient, Pseudomonas aeruginosa and Candida albicans in 1 patient, and Candida albicans in 1 patient). All patients were successfully treated with fluid replacement and antimicrobial therapy. Bacteraemia and candidaemia appear to be a considerable and underestimated complication of severe rotavirus gastroenteritis.