Bardet-Biedl syndrome (BBS) is a rare autosomal recessive disorder known to be caused by mutations in at least 19 BBS genes. We report the genetic analysis of a patient with indisputable features of BBS including cardinal features such as postaxial polydactyly, retinitis pigmentosa, obesity, and kidney failure. Taking advantage of next-generation sequencing technology, we applied whole exome sequencing (WES) with Sanger direct sequencing to the proband and her unaffected mother. A pair of heterozygous nonsense mutations in BBS2 gene was identified in the proband, one being novel and the other recurrent. The novel mutation, p.Y644X, resides in exon 16 and was also found in the heterozygous state in the mother. This mutation is not currently found in the dsSNP and 1000 Genome SNP databases and is predicted to be disease causing by in silico analysis. This study highlights the potential for a rapid and precise detection of disease causing gene using WES in genetically heterogeneous disorders such as BBS.