Recent studies have found evidence of retinal thinning in schizophrenia spectrum disorder patients; however, it is not known whether retinal thinning is present at the first episode of psychosis or whether it is a result of the progression of the disease or related factors (e.g., emergence of medical comorbidities). We hypothesized that first episode patients (FEP) would not differ on any retinal variables when compared to age matched controls, while chronically ill patients would show evidence of retinal thinning compared to age matched controls. 15 first episode patients, 20 control subjects age-matched to the FEP group, 18 chronically ill patients, and 18 control subjects age-matched to the chronically ill group participated in Spectral Domain OCT scans. We collected data on retinal nerve fiber layer (RNFL) thickness, macula thickness and volume, and ganglion cell-inner plexiform layer (GCL-IPL) thickness as well as cup-to-disc ratio at the optic nerve head. No evidence of retinal structural change was found in the first episode group. In contrast, chronic schizophrenia and schizoaffective disorder patients were characterized by GCL-IPL thinning and overall macula thinning and volume reduction. No evidence of RNFL thinning was observed in the chronic group, however. These data suggest that retinal structure is unaffected very early in the course of schizophrenia spectrum disorders but that thinning is an aspect of illness progression, medical comorbidity, and/or long-term antipsychotic medication use in schizophrenia spectrum disorders. Among retinal indices, macula thickness and volume appear to be the most sensitive to the changes associated with illness chronicity.