Comorbidity of substance use disorders (SUD) and severe mental illness (SMI) is highly frequent in patients, the most common diagnoses being schizophrenia (SZ), bipolar disorder (BD) and major depressive disorder (MDD). Since comorbidity has its own clinical features, and neurocognitive functioning is not always similar to psychiatric symptoms the present study explores the cognitive performance of patients with dual disorders. A neuropsychological battery of tests was used to assess 120 under treatment male patients, 40 for each group considered (SZ + SUD, BD + SUD and MDD + SUD) who were mainly polyconsumers. Significant differences (with premorbid IQ as a covariate) were found among the groups, with SZ + SUD having a worse performance in attention, verbal learning, short term memory and recognition. The consideration of a global Z score for performance evidenced an impaired neurocognitive pattern for SZ + SUD compared with BD + SUD and MDD + SUD. According to norms, all patients showed difficulties in verbal learning, short-term memory and recognition. Our research indicated that the neurocognitive functioning of dual disorder patients was influenced by the comorbid SMI, with SZ + SUD presenting major difficulties. Future studies should thoroughly explore the role of such difficulties as indicators or endophenotypes for dual schizophrenia disorders, and their usefulness for prevention and treatment.