AimsIn 1996 a Hong Kong-wide survey of pharmacological treatment for schizophrenic inpatients identified a few idiosyncratic prescription patterns that were not consistent with international standards. In the context of continuous quality assurance, the survey was repeated in 1999 to monitor trends in the pharmacotherapy of schizophrenia and to identify changes in prescribing practices. It was expected that the widespread introduction of novel antipsychotic drugs coupled with continuing medical education would favourably alter prescribing habits. Methods A representative random sample of 1202 schizophrenic patients from all inpatient settings in Hong Kong was surveyed. Basic socio-demographic data and a list of all psychotropic medication taken on census day were collected. Results Significant improvement was noted in several aspects of pharmacotherapy in 1999 as compared with 1996. The total daily dosage of antipsychotic drugs decreased from 716 ± 627 to 561 ± 482 mg day − 1 chlorpromazine equivalent (CPZeq) (Mann-Whitney U -test; Z = − 3.906, P = 0.000; 95% confidence interval [CI] = 70.0, 240.2 mg day − 1 CPZeq), for acute patients and from 923 ± 809 to 675 ± 545 mg day − 1 CPZeq (Mann-Whitney U -test; Z = − 5.036, P = 0.000; 95% CI = 175.57, 321.63 mg day − 1 CPZeq) for chronic patients. The percentage of patients coprescribed antipsychotics and an antiparkinson drug significantly decreased from 67.8% to 61.8% ( χ 2 = 5.558, P = 0.018) in the chronic schizophrenia group. The percentage of patients taking atypical antipsychotic medication increased significantly from 5.5% to 19.2% ( χ 2 = 27.14, P = 0.000) in the acute and 3.4% to 12.3% ( χ 2 = 27.76, P = 0.000) in the chronic group. Conclusions Repeated surveys of prescribing practices proved to be a useful tool to demonstrate trends in the pharmacological treatment of schizophrenia. Our findings suggest that the widespread use of atypical antipsychotic drugs contributed to a more rational pharmacotherapy for schizophrenia.