Abstract A polymorhism in the 5′ region of the serotonin transporter gene modulates its transcription efficiency. Its short allele has been reported to be associated with neurotic traits. The serotinin transporter is the action site of selective serotonine re-uptake inhibitors, widely used in the treatment of panic disorder. We examined an association between the polymorphism and panic disorder in a case-control study consisting of 66 Japanese patients and 150 controls. The short allele was significantly more frequent in the Japanese than in Caucasians. The patients and the controls had similar allele frequencies, indication no association between the polymorehism and panic disorder in most Japanese patients.