Executive dysfunction is a core deficit in schizophrenia (SCH). However, some controversy exists when examining such deficits in studies of bipolar disorder (BD). The aim of the present research was to investigate whether executive deficits were similar or distinct in both illnesses. 148 patients with BD, 262 patients with stable SCH and 108 healthy controls (CT) were recruited for the study. The BD patients were also differentiated according to the clinical subtype (BD subtype I, BDI, or subtype II, BDII) they exhibited and according to whether there was a previous history of psychosis. All subjects completed a broad neuropsychological battery. The influences of other clinical data were also evaluated. Both the BD and SCH patients showed widespread deficits in all executive tasks, with no differences between these two groups of patients. BDII patients only showed some selective deficits, and their scores on planning and inhibitory tasks fell on the continuum between the CT, the BDI and the SCH patients. Psychotic phenotypes did not influence the BD patients' performance on the battery. Other clinical variables related to illness severity did influence deficits in any subgroup of patients. Our results point to the existence of common executive disturbances in both diagnostic categories. Moreover, the inclusion of subclinical phenotypes in research may be helpful in cognitive assessment studies.