A nosological issue that has yet to be resolved relates to the diagnostic and clinical overlap of schizophrenia and schizoaffective disorder. Thus, the aim of this study was to compare, within a treated epidemiological cohort of first episode patients, the clinical characteristics of patients with schizophrenia (FES) or schizoaffective disorder (FESA). Medical fi le audit methodology was employed to collect information on 704 first episode psychosis patients (FEP), among which 283 patients had a fi nal diagnosis of FES and 64 patients with a fi nal diagnosis of FESA. These patients were treated at the Early Psychosis Prevention and Intervention Centre (EPPIC), Melbourne, Australia. Patients with FES were signifi cantly more likely to have a longer prodrome (P = .020), longer duration of untreated psychosis (P < .001), and earlier age of onset (P = .004) compared to FESA. At service entry, FESA patients had more severe levels of psychopathology (P = .020), which was due to the presence of manic symptoms (P < .001); consequently, requiring a greater number of inpatient admissions (P = .017). At discharge, depressive symptoms were more severe in those with FESA (P = .011). There are signifi cant differences in the phenomenology of schizophrenia and schizoaffective disorder during early illness course; supporting the notion that these are two discernable disorders.