Population genetic studies in Roma population have characterised it as a young genetic isolate, with limited genetic diversity, strong founder effect for many mendelian disorders and a complex sub-isolate structure. As suggested by previous studies of isolated populations, they could offer some advantages in the search of genes contributing to complex genetic disorders as well. Recent linkage analysis of genome-scan and fine mapping data provided best evidence for linkage between bipolar affective disorder (BPAD) and loci on chromosomes 1p36, 2p14-p16, 4q31, and 6q24 in three large families of Roma descent. All additional loci showing suggestive evidence of linkage in the genome scan (8p21, 9p23, 11p13, 13q31, 17q23, and 18q12) we subjected to a systematic fine mapping study. To deal with the problem of statistical analysis of the extended pedigrees, including new affected members and branches, both Genehunter and Sim Walk2 were used and the results compared. Higher-density mapping provides additional support for BPAD susceptibility loci on 4q31 and 6q24. Suggestive evidence for linkage is confirmed for 11p13, 13q31 and allows further narrowing down of the linkage regions. Genetic heterogeneity, both intra and inter-familiar is observed even within this small set of families.