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.