A role for the serotonin transporter (5-HTT) gene polymorphism in mental illnesses and anxiety-traits has been implicated. The contribution of genetic factors in personality traits and the manifestation of specific symptoms in psychiatric illnesses have yet to be elucidated. Anxious-depressive symptoms are a significant component in a pattern of schizophrenic symptoms. This study focused on the relation between 5-HTT polymorphism and clinical presentations of schizophrenia, specifically those related to the affective spectrum. Using clinical and psychological analyses, we tested the genetic association between the 5-HTTLPR polymorphism (5-HTT gene-linked polymorphic region) and anxiety- and depressive-related symptoms emerged in schizophrenia. In 260 patients with an ICD-10 diagnosis of schizophrenia (broad definition), we studied the 5-HTTLPR genotype (insertion-deletion polymorphism), the Positive and Negative Syndrome Scale (PANSS), and self-rated inventories (EPI, MMPI, STAI) scores. Patients with the "ss" genotype (deletion variant) scored significantly higher on "Guilt feelings" and "Depression" items, as compared with those of the "ll" genotype (insertion variant) (P = 0.016, 0.039, respectively). The frequency of the "ss" genotype was reduced in patients with no depression or guilt feelings, or in those patients exhibiting questionable symptoms. In contrast, the "ss" genotype carriers prevailed among the patients with mild, moderate, or severe ratings of the symptoms. The scores on all anxiety- and depression-related traits, self-rated by the patients, did not significantly differ by genotype. Our finding may contribute to understanding of molecular genetic features underlying an appearance of psychopathological symptoms emerged in schizophrenia.