Cell fusion studies using lymphoblastoid cell lines from Fanconi anaemia (FA) patients have identified five complementation groups (FA-A to FA-E) among European FA patients. In Italy, of the 45 FA families referred to the Italian Registry of Fanconi Anaemia (RIAF), 15 took part in a project for the identification of complementation groups. Since three immortalized lymphoblast lines were resistant to a cross-linking agent, we analysed only 12 patients by complementation analysis and found that 11 belong to complementation group A. Four and seven families came from two geographic clusters in the Veneto and Campania regions, respectively, which are thought to consist of aggregates of related families in reproductive isolation. The clinical characteristics of the patients showed both intra- and interfamilial heterogeneity, although overall the disease had a relatively mild course. Since the populations in both Veneto and Campania are likely to represent genetic isolates, our finding predicts linkage disequilibrium for markers flanking the FAA gene. DNAs from these FA families may thus be utilized for positional cloning of this gene through haplotype disequilibrium mapping.