STUDY OBJECTIVE: To estimate the prevalence of injecting drug use (IDU) in three cities in England and to measure the coverage of key public health indicators. DESIGN: Capture-recapture techniques with covariate effects. SETTING: Liverpool, Brighton, and 12 London boroughs, 2000/01. PARTICIPANTS: IDU collated and matched across five data sources-community recruited survey, specialist drug treatment, arrest referral, syringe exchange, and accident and emergency-896 in Brighton, 1224 in Liverpool, and 6111 in London. MAIN RESULTS: It is estimated that in 2000/01 the number and prevalence of IDU aged 15-44 was 2300 (95%CI 1500 to 3700) and 2.0% (95%CI% 1.3% to 3.2%) in Brighton; 2900 (95%CI 2500 to 5000) and 1.5% (95%CI 1.3% to 2.6%) in Liverpool; 16 700 (95%CI 13 800 to 21 600) and 1.2% (95%CI 1.0% to 1.6%) in 12 London boroughs; with a prevalence of 1.7% (95%CI 1.2% to 3.3%) in inner London. It is estimated that: less than one in four IDU are in treatment in the three areas; syringe exchange programmes covered about 25% of injections in Brighton and Liverpool and 20% in London; and that the annual opioid mortality rate among IDU was 2% in Brighton compared with less than 1% in Liverpool and London. CONCLUSIONS: Credible estimates of the prevalence of injecting drug use (and key public health indicators) can be determined using covariate capture-recapture techniques. These suggest that: targets to double the number in treatment are possible: syringe distribution should be increased; and further attention, especially in Brighton, given to reducing overdose mortality.