The French Institute for Public Health Surveillance (InVS) is responsible for the national coordination of the surveillance system for notifiable diseases. The objective of this system is to detect and report the 31 notifiable diseases in order to take action and prevent the risk of epidemics, as well as to analyze trends in these diseases over time. The report provides an overview of the 29 notifiable infectious diseases between 2005 and 2009 in Franche-Comté. Between 2005 and 2009, 913 notifiable diseases were reported in the Franche-Comté region. The top three reported diseases were tuberculosis (32% of MDOs), Legionnaires’ disease (26% of MDOs), and HIV infections (15% of MDOs). All other MDOs accounted for less than 10%. Most MDOs systematically require investigations to ensure that the risk of human-to-human transmission is controlled, with the support of clinicians and the relevant services. This report contributes to providing feedback to all reporting entities. (R.A.)