Many problems exist in the surveillance of human food-borne illnesses, and one of the most important is identifying the responsible microorganisms. For this reason, a survey was carried out to identify regional reference laboratories and laboratories with the capacities necessary for identification of pathogenic microorganisms in Italy. All 21 Italian regions and autonomous provinces completed the survey except three (Basilicata, Tuscany and Sardinia).Only 6% of the identified laboratories were found to have been formally designated as regional reference laboratories. Seventy-one percent of all laboratories reported having the capacity to diagnose over half (>7/13) of the listed bacteria, 69% over half of the listed parasites (> 4/8) and 51% over half of the listed viruses (>2/4). No differences were found in the capability to diagnose bacterial and parasitic infections, between laboratories in northern, central and southern Italy, while a significant difference was found in the capability to diagnose viral infections between laboratories in the three geographical areas (p <0.01). This study clearly shows that there is a need to improve diagnostic capacities of regional reference laboratories and laboratories involved in the surveillance of food-borne illnesses in Italy.