The primary objective of this first study in Franche-Comté is to estimate the incidence of seven tick-borne diseases (Lyme disease, tick-borne encephalitis, granulocytic anaplasmosis, TIBOLA, LAR, tularemia, and Q fever). Between April 1, 2010, and March 31, 2012, a network of physicians (general practitioners and specialists) reported all newly diagnosed cases of these diseases to the Regional Intervention Unit (Cire). The validation and classification of Lyme borreliosis cases (confirmed, probable, and excluded cases) were performed by a committee of experts using case definitions derived from a European consensus (European Concerted Action on Lyme Borreliosis - EUCALB). Training sessions were organized during the study. The overall participation rate among physicians was 12% and remained consistent over the 24-month period. Of the 604 reports, 432 (71%) met the epidemiological definition of a confirmed or probable case of Lyme borreliosis. The majority of confirmed or probable cases were isolated erythema migrans. No reports of other tick-borne diseases were accepted by the expert committee. The number of new cases of Lyme borreliosis was estimated at approximately 2,000 cases over the two years of the study, bringing the average annual incidence rate to 85 cases per 100,000 inhabitants (95% CI [77–92]). The estimated incidence rate in the first year (April 1, 2010, to March 31, 2011) was slightly lower than in the second year (74, 95% CI [65–84] vs. 95 per 100,000 inhabitants, 95% CI [83–108]). Incidence rates vary by department and subregion.