Injecting drug users (IDUs) have a direct social and economical impact, yet can typically be regarded as a hidden population within a community. We estimate the size of the IDU population across the nine different Government Office Regions of England in 2005/6 using capture-recapture methods with age (ranging from 15-64) and gender as covariate information. We consider a Bayesian model-averaging approach using log-linear models, where we are able to include explicit prior information within the analysis in relation to the total population size (elicited from the number of drug-related deaths and injectors’ drug-related death rates) and the male to female ratio of IDUs. Estimating the data at the regional level allows for regional heterogeneity and was aggregated to obtain an estimate at the England level with posterior mean of 196700 and 95% credible interval (183350, 211000), estimated to nearest 50. The results show significant regional variability in the estimated prevalence of current IDUs (with posterior means ranging from 3 to 9 per 1000 of population aged 15-64) and injecting drug-related death rates across the gender × age cross-classifications.