The present study aimed to compare population-based familial samples of patients with schizophrenia (n = 218) and schizoaffective disorder (n = 62) and a healthy control group (n = 123). Patients with schizoaffective disorder outperformed patients with schizophrenia in verbal ability, processing speed, visual working memory, and verbal memory. When compared with controls, patients with schizoaffective disorder also had a generalized cognitive impairment. Adjusting for clinical characteristics removed significant differences between the patient groups. Irrespective of the diagnosis, patients with the most severe negative symptoms and highest dose of antipsychotics had the most severe cognitive impairments, whereas mood symptoms were not related to cognitive performance. In conclusion, people with schizoaffective disorder have severe cognitive impairments, but the impairments are milder than in schizophrenia. Mood symptoms may not explain the difference between the diagnostic groups in cognitive functions, but the difference may be related to differences in the severity of negative symptoms.