Context and objective: In France, national estimates of the incidence of cancers are based on mortality data by extrapolating the ratio between observed incidence and mortality in areas covered by cancer registries. The objective of this study is to determine the interest of using the discharge abstracts database gathered in hospitals to estimate breast cancer incidence in two French departments: Côte d'Or and Doubs. Methods: This study concerns the incident breast cancer cases identified in 2004 and 2005 through Côte d'Or and Doubs cancer registries and potential incident breast cancer cases selected through two algorithms in the Medical Information System Program (PMSI – Programme de Médicalisation des Systèmes d'Information) databases. The value of these algorithms was evaluated by probabilistic linkage between data from the anonymous registry and from the PMSI. Results: The first algorithm provides an estimated incidence close to those given by registries, and has a good sensitivity and positive predictive value; the second algorithm overestimates the incidence by about 100%, and has a poor positive predictive value. Conclusion: This study shows the usefulness of the PMSI databases and underlines the interest and difficulties of using these data to estimate cancer incidence. The PMSI database cannot be used as a unique source to estimate breast cancer incidence.