Diarrhoeal illnesses are the most frequent of notifiable diseases in Aragon. Physicians notify diarrhoea cases with presumed infectious origin on a weekly basis. Following an increase in 2005–2006, we aimed to identify the responsible organism(s) in order to inform control measures. We described seasonality of diarrhoea notifications for 1998–2004 and 2005–2006. We calculated correlations between diarrhoea notifications and enteric pathogens diagnosed in two Aragonese laboratories, and applied linear regression using coefficients of determination (r2). In 2005–2006 the winter peak of diarrhoea notifications increased from 2494 to 3357 weekly cases (34·6%) and the peak in Rotavirus diagnoses from 15 to 39 weekly cases. The correlation of diarrhoea notifications with Rotavirus was 0·05 in 1998–2004 and 0·42 in 2005–2006. The model for 1998–2004 included Salmonella enterica, Giardia lamblia and Clostridium difficile (r2=0·08) and for 2005–2006 Rotavirus and Astrovirus (r2=0·24). Our results suggest that Rotavirus contributed to the increase of diarrhoea notifications. We recommend determining the disease burden of Rotavirus in order to guide vaccination policies.