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Objective: To determine the incidence of chronic diseases (ALD30) in the French armed forces between 2005 and 2011. Methods: Descriptive study on active soldiers covered by the French military healthcare system (CNMSS) between 01/01/2005 and 31/12/2011. Data were standardized due to over-representation of young men. The incidence of ALD30 was analyzed from medical records by consulting physicians using the Hippocrate database. Results: The mean annual population comprised 331,000 persons. During the study, 10,107 of the 11,581 soldiers to whom an ALD diagnosis was attributed were granted exemption of co-payment. The mean age was 43.2 years, 87.9% of patients were male. The most common chronic diseases were cardiovascular diseases, representing 29.8% of the group, followed by malignant tumours (24.3%), diabetes (14.8%) and severe psychiatric disorders (8.6%). The age-matched standard incidence rate of was higher for women than for men (501 vs 462 per 100,000). The Army had the highest standard incidence rate of ALD and the Navy had the lowest incidence rate (1,139 vs 768 per 100,000).In comparison with the age- and gender-adjusted incidence rates in the general population, the armed forces almost always presented a much lower risk of ALD, which could be explained by medical selection, the type of activity and the short-term affiliation of the users of CNMSS. Conclusion: Data extracted from ALD databases are useful for epidemiological studies and for the evaluation of health and prevention programmes.