BACKGROUND The Italian database of factor IX gene (F9) mutations has been built since 2001 and is, so far, the most practical instrument for comprehensive genetic counselling, carrier detection and prenatal diagnosis. Over time the haemophilia B database has been enriched by entries on a larger number of patients and molecular genetic data identifying heterogeneous mutations spanning the entire F9. METHODS Conformation sensitive gel electrophoresis is a variant of heteroduplex analysis, which has been applied for screening F9 for mutations, which are further fully characterised by direct sequencing of the amplified mutated regions. This project has involved 29 Italian haemophilia centres and provides data concerning the analysis of a cohort of 306 unrelated patients with haemophilia B (191 with severe, 67 with moderate and 48 with mild disease, including 8 patients with severe haemophilia B with inhibitors). The recorded data include levels of factor IX clotting activity, inhibitor status and clinical severity. RESULTS Detailed analysis of the mutations revealed 164 different mutations, that are considered as unique molecular events (8 large deletions, 11 small deletions, 1 combined deletion/ insertion, 2 insertions, 104 missense, 20 nonsense, 14 mutations in a splicing site, 3 in the promoter and 1 silent). The data recorded in the Italian F9 mutation database provided the basis to study 85 families with haemophilia B, involving 180 females (20 obligate carriers, 106 carriers and 54 non-carriers) and enabled 14 prenatal diagnoses to be made in 12 females. CONCLUSIONS Genetic analysis is required to determine female carrier status reliably. Female relatives may request carrier analysis, when a male relative is first diagnosed as having haemophilia or when they are pregnant. At present, the data collected in the Italian national register of mutations in haemophilia B provide the opportunity to perform prompt and precise determination of carrier status and prenatal diagnosis by specific mutation analysis.