Background: To assist with the development of a French online quality-controlled health gateway(CISMeF), an automatic indexing tool assigning MeSH descriptors to medical text in French was created. The French Multi-Terminology Indexer (FMTI) relies on a multi-terminology approach involving four prominent medical terminologies and the mappings between them. Objective: In this paper,we compare lemmatization and stemming as methods to process French medical text for indexing. We also evaluate the multi-terminology approach implemented in F-MTI. Methods: The indexing strategies were assessed on a corpus of 18,814 resources indexed manually. Results: There is little difference in the indexing performance when lemmatization or stemming is used. However, the multi-terminology approach outperforms indexing relying on a single terminology in terms of recall.Conclusion: F-MTI will soon be used in the CISMeF production environment and in a Health MultiTerminology Server in French.