In March 2012, there was an unusual increase of gastroenteritis cases in a district with 37 264 inhabitants in central Greece. It was estimated that more than 3600 people developed symptoms. A 1:1 case-control study showed that consumption of tap water was a risk factor for acquiring infection [odds ratio (OR) 2·18, 95% confidence interval (CI) 1·11–4·28]. Descriptive data, low gastroenteritis incidence in adjacent areas with different water supply systems, and water-quality data further supported the hypothesis of a waterborne outbreak. Thirty-eight stool samples were positive for rotavirus. Bacterial indicators of recent faecal contamination were detected in samples from the water source and ice cubes from a local production enterprise. Molecular epidemiology of rotavirus strains, apart from the common strain, G3[P8], identified the unusual G/P combination G2P. Water sanitation measures contributed to the control of the outbreak. This outbreak demonstrated the need for the cooperation of laboratories with different expertise and the importance of early notification of waterborne gastroenteritis outbreaks.