Cognitive functioning in the nonsymptomatic phase and the long-term cognitive outcome of patients with mood disorders are both heuristic and important clinical issues in the study of mood disorders. Literature findings are inconsistent because of design confounds. We tried to address these issues while controlling for several confounds including age, education, gender differences in neurobehavioral functioning, and diagnosis. Nonsymptomatic patients with a history of chronic unipolar depression and bipolar affective disorder and healthy male individuals were administered neuropsychological tests to assess attention, visual-motor tracking, executive abilities, and immediate verbal memory. Subjects had comparable depression scores at the time of testing. Disease duration was 7.5 years (SD 5.1) for unipolar and 11 years (SD 7.3) for bipolar patients. Unipolar patients were more impaired than healthy normal comparison subjects on measures of visual-motor sequencing (Trail Making Test A, p < .05), executive function (Trail Making Test B, Stroop Test Color/Word Trial, p < .05), and immediate memory and attention (CERAD 1st trial, WAIS Digit Symbol subtest, p < .05). Differences between bipolar patients and normal comparison subjects did not reach significance in any of the selected measures. Male patients with a history of chronic unipolar disorder are at risk for cognitive impairment in the nonsymptomatic phase of their disease. Cognitive disturbance is the type seen with prefrontal dysfunction and may be assessed with standard neuropsychological assessments.