This paper tackles the problem of term ambiguity, especially for biomedical literature. We propose and evaluate two methods of Word Sense Disambiguation (WSD) for biomedical terms and integrate them to a sense-based document indexing and retrieval framework. Ambiguous biomedical terms in documents and queries are disambiguated using the Medical Subject Headings (MeSH) thesaurus and semantically indexed with their associated correct sense. The experimental evaluation carried out on the TREC9-FT 2000 collection shows that our approach of WSD and sense-based indexing and retrieval outperforms the baseline. Key words: Word Sense Disambiguation, Semantic Indexing, Term Weighting, Biomedical Information Retrieval