Suicidal behavior in schizoaffective disorder is a serious problem and suicide risk during lifetime ranges between 5%–10%. Neurobiology of suicidal behavior has not been studied sufficiently, and a high number of studies are oriented toward lipid investigation. The aim of our study was to investigate whether there were differences in the level of lipids (cholesterol, HDL-cholesterol, LDL-cholesterol, triglycerides) in hospitalized suicidal ( n = 20) and non-suicidal ( n = 20) patients with schizoaffective disorder. The study also included male healthy control subjects ( n = 20). Hamilton Depression Rating Scale (HDRS-17), and Positive and Negative Syndrome Scale (PANSS) were used to confirm the level of psychopathology in patients with schizoaffective disorder. Severity of suicidality was measured by Scale for Suicide Ideation (SSI) at time of admission. Results of the study indicated significantly lower concentrations of cholesterol ( p < 0.001), LDL-cholesterol ( p < 0.01) and HDL-cholesterol ( p < 0.01). There were no differences in the number of previous hospitalization and previous suicide attempts between suicidal and non-suicidal patients ( p > 0.05). Duration of the illness was significantly ( p < 0.05) shorter in suicidal patients. Suicidal patients also had a significantly higher score on HDRS-17 ( p < 0.001) and PANSS ( p < 0.01) compared to non-suicidal patients.