Background: A neurobiologically informed, system-specific psychopathological approach has been suggested for use in schizophrenia. However, to our knowledge, such an approach has not been used to prospectively describe the course of schizophrenia. Sampling and Methods: We assessed psychopathology in a well-described sample of 100 patients with schizophrenia or schizoaffective disorder with the Bern Psychopathology Scale (BPS) at 6-month intervals for up to 18 months. The BPS groups symptoms into the 3 domains language, affectivity and motor behaviour; each domain is rated as being normal, inhibited or disinhibited. In addition, we collected qualitative psychopathological data in the form of case reports. Results: Forty-eight patients completed at least 2 assessments over the course of at least 1 year. Of these, 16 patients (33.3%) showed a bipolar course pattern (i.e., a switch from inhibited to disinhibited or vice versa) in 1 domain and 6 patients (12.5%) in more than 1 domain. Shifts from 1 dominant domain to another were seen frequently (n = 20, 41.7%), but shifts between 1 dominant domain and a combination of dominant domains were more common (n = 33, 68.8%). Conclusions: The course of schizophrenia is heterogeneous and shows frequent changes in psychopathology. This should be taken into account in the communication with patients and in the research on underlying illness mechanisms and treatment. A major limitation of this study is the small sample size.