Aims. To estimate the prevalence of opiate or benzodiazepine misuse in the Grampian Health Board area, Scotland and illustrate the use of the capture-recapture method in both rural and urban settings. Design. Capture-recapture analyses on six distinct sources of data with unequal coverage of the geographical area. Setting. Grampian Health Board area, including the City of Aberdeen. Participants. Data were collated from the Police, Social Work Departments, GPs contributing to the Scottish Drug Misuse Database, statutory drug agencies, a voluntary sector drug agency and a needle/syringe exchange. Measurements. In total 1770 individuals were identified as misusing opiates or benzodiazepines and residing in the Grampian Health Board area; 1129 individuals were resident in the City of Aberdeen. Findings. The total number of opiate or benzodiazepine misusers in the City of Aberdeen was estimated to be 2519 (95% CI 2048-3200). This figure corresponds to 2.0% (1.6-2.5%) of the population aged 15-54 years. In a town to the north of Aberdeenshire where high levels of heroin use had previously been reported in the media, 2.5% of the population aged 15-54 (1.8-3.8%) were estimated to be misusing opiates or benzodiazepines. Conclusions. Although there may be difficulties in applying capture-recapture methods in all settings, the methodology can give valuable information on the extent of drug misuse in both urban and non-urban areas. This information is particularly important to assess the spread of drug misuse from cities to rural areas.