Introduction Schizophrenia is a debilitating mental disorder with similar prevalence across different cultures and geographical regions. The prevalence of schizophrenia and non-affective psychosis has previously been shown to vary by age, gender and socio-economic status in a subset of the Stockholm county population. Objectives To investigate the entire Stockholm county population of patients with schizophrenia and non-affective psychosis regarding variations in age, gender, socio-economic status and pharmacological treatment. Aims To gather reliable data to guide decision-makers in the optimal allocation of resources. Methods Individuals with a registered diagnosis of non-affective psychosis (ICD-10 F20 – F29) between 1/1 2000 and 31/12 2012 with any contact with the Stockholm regional health care in 2012 were identified in the regional health care data warehouse (VAL). Data regarding outpatient visits in primary and specialist care, hospitalizations and dispensed prescriptions were retrieved. Results Of the study population containing 18000 patients with non-affective psychosis, 34% had a schizophrenia diagnosis. 56% of the schizophrenia patients were men. The highest prevalence was observed in the 50 – 59 year olds, followed by 40 – 49 year olds. The schizophrenia prevalence was higher in municipalities of lower socio-economic status within the Stockholm county. A similar pattern for nonaffective psychosis patients was observed. The difference in prevalence was considerably smaller between the municipalities for the nonaffective patient population than for the schizophrenic patient population. Conclusions This study population will provide new insights into the burden of disease of psychosis diagnoses as demonstrated by differences in prevalence from various aspects.