Background: We investigated antipsychotic drug prescription practice of Dutch ID physicians, studying prevalence of antipsychotic drug use, reasons for prescription and the relationship between these reasons and patient characteristics. Methods: A cross-sectional study of medical and pharmaceutical records in a population living in residential settings of three care providers for persons with IDs in the Netherlands (n = 2373). Results: Prevalence of antipsychotic drug use was 32.2% (95% CI 30.1-33.9). Behavioural problems were the reason for prescription of antipsychotic drugs in 58% of cases and psychotic disorder or psychotic symptoms in 22.5%. In 11.7% the diagnosis of psychotic disorder was specified according to DSM-IV criteria. In 18.5% the reason for prescription was not noted in the medical record. Behavioural problems as reason for prescription was associated with profound and severe ID, living in a central location and male sex. Psychotic disorder specified according to DSM-IV as indication for prescription was negatively associated with profound and severe ID and with presence of an additional mental disorder. Absence of a noted reason for prescription was associated with female sex and with the presence of an additional mental disorder. Discussion: Current prevalence and reason for prescription of antipsychotic drugs are similar with outcomes of previous studies. Our results show the continuing lack of evidence-based psychopharmacological treatment in mental health care for persons with IDs.