Mood disorders include major depressive disorder and bipolar disorder. They are complex psychiatric disorders that are the leading cause of disability to work in Finland. The principle aim of this investigation was to characterize the genetic background of mood disorders and heir endophenotypes in Finnish mood disorder samples. Association was observed between mood disorders and BDNF, SLC6A4, and P2RX7 genes; clinical outcome of patients and functional variants of the P2RX7 gene; and the general intellectual functioning and DAOA gene. The effort to replicate the results from the first GWA studies revealed five genomic areas that associated with mood disorder and with some potential mood disorders endophenotypes. This thesis provides information about the genetic background of mood disorders in Finland and it also reveals some potential endophenotypes, or trait features, that might convey the effect of the suspectibility genes to the end diagnosis of mood disorder.