Akita Prefecture, Japan, has consistently recorded the highest level of suicide rates in all of Japan. In this study, we attempted to determine whether genetic differences between suicide victims and the normal population in Akita exist. We also researched the geographical differences in polymorphisms of the genes between people living in Akita Prefecture and those living in other prefectures with lower suicide rates as recorded in previously-published studies. Specifically, we investigated two serotonin-related genes including three substitutions connected to human emotional states such as despondency and depression: the tryptophan hydroxylase (TPH) gene (A779C and A218C in the intron) and the serotonin1A (5-HT_1A) receptor gene (Pro16Leu in the cording region). 134 suicide victims and 325 healthy volunteers were examined. For this process, we used two analytical procedures: (1) polymerase chain reaction (PCR) followed by single-strand conformational polymorphisms analysis for the A779C of TPH and the 5-HT_1A receptor genes and (2) PCR followed by restriction fragment length polymorphism analysis for the A218C of TPH gene. No significant differences of the genotypes and the allele frequencies between the suicide samples and those of the healthy controls were discerned. Moreover, the genotype distributions of the TPH and 5-HT_1A receptor genes were compared between Akita Prefecture and other prefectures, but no significant differences were found. In conclusion, no significant relation could be established statistically concerning the serotonin related genes between the suicide samples and control samples in Akita.