Congenital malformations occur in about 2 % of newborn babies and differ in nature and severity. The parents usually ask questions about the cause, the recurrence risk, the treatment and the long-term result as adults. The project aims at answering some of these questions for some malformations. To be able to answer questions on cause and recurrence risk we perform molecular studies of hypospadias and other disorders of sex development (DSD), bladder exstrophy and intestinal malrotation. We aim to identify genes for these malformations by genetic analysis like linkage, association studies, mutation screening, whole exome/ genome sequencing and array CGH of isolated and familial cases. The results will increase the knowledge about the pathogenesis of these disorders as well as the long term outcome for these patients and thus will enable us to give better information to patients and their families in the future. We have collected DNA from 130 patients with bladder exstrophy and parents to about half of them. We have over 100 smaller families with hypospadias and infantile hypertrophic stenosis. Currently, we have whole genome sequence (WGS) data at UPPMAX for 20 human trios and we are planning to conduct additional WGS or whole exome sequencing in DNA samples from cases with other malformations.