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.