Background: Utilization of diagnostic information from national patient registries rests on the quality of the registered diagnoses. We aimed to investigate the agreement and consistency of diagnoses of psychotic and bipolar disorders in the Norwegian Patient Registry (NPR) compared to structured interview-based diagnoses given as part of a clinical research project. Methods: Diagnostic data from NPR were obtained for the period 01.01.2008-31.12.2013 for all patients who had been included in the Thematically Organized Psychosis (TOP) study between 18.10.2002 and 01.09.2014 with a Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV) diagnosis of schizophrenia (n = 537), delusional disorder (n = 48), schizoaffective disorder (n = 118) or bipolar disorder (n = 408). Diagnostic agreement between the primary DSM-IV diagnosis in TOP and the International Classification of Diseases, 10th revision (ICD-10) diagnoses in NPR was evaluated using Cohen's unweighted nominal kappa (K). Diagnostic consistency was calculated as the proportion of all registered severe mental disorder diagnoses in NPR that were equivalent to the primary diagnosis given in the TOP study. Results: The proportion of patients registered with the equivalent ICD-10 diagnosis as the primary DSM-IV diagnosis given in TOP was 84.2% for the schizophrenia group, 68.8% for the delusional disorder group, 76.3% for the schizoaffective disorder group, and 78.4% for the bipolar disorder group. Diagnostic agreement was good for schizophrenia (K = 0.74) and bipolar disorder (K = 0.72), fair for schizoaffective disorder (K = 0.63), and poor for delusional disorder (K = 0.39). Among patients with DSM-IV schizophrenia, 4.7% were diagnosed with ICD-10 bipolar disorder, and among patients with DSM-IV bipolar disorder, 2.5% were diagnosed with ICD-10 schizophrenia. Diagnostic consistency was 84.9% for schizophrenia, 59.1% for delusional disorder, 65.9% for schizoaffective disorder, and 91.0% for bipolar disorder. Conclusions: When compared to research-based diagnoses, clinical diagnoses of schizophrenia and bipolar disorder in the NPR are accurate and consistent, with minimal diagnostic overlap between the two disorders.