Aims: Here we report a study aimed at estimating trends in the prevalence of injection drug use between 2005 and 2009 in Estonia. Background: Descriptions of behavioural epidemics have received little attention compared with infectious disease epidemics in Eastern Europe. Methods: The number of injection drug users (IDUs) aged 15–44 each year between 2005 and 2009 was estimated using capture–recapture methodology based on 4 data sources (2 treatment data bases: drug use and non-fatal overdose treatment; criminal justice (drug related offences) and mortality (injection drug use related deaths) data). Poisson log-linear regression models were applied to the matched data, with interactions between data sources fitted to replicate the dependencies between the data sources. Linear regression was used to estimate average change over time. Results: There were 24305, 12,292, 238, 545 records and 8100, 1655, 155, 545 individual IDUs identified in the four capture sources (police, drug treatment, overdose, and death registry, accordingly) over the period 2005–2009. The estimated prevalence of IDUs among the population aged 15–44 declined from 2.7% (1.8–7.9%) in 2005 to 2.0% (1.4–5.0%) in 2008, and 0.9% (0.7–1.7%) in 2009. Regression analysis indicated an average reduction of about 1600 injectors per year. Conclusion: While the capture–recapture method has known limitations, the results are consistent with other data from Estonia. Identifying the drivers of change in the prevalence of injection drug use warrants further research.