Background: To estimate the prevalence of problem drug use (PDU) and injecting drug use (IDU) in Luxembourg and analyze trends between 1997 and 2009. To assess the feasibility of prevalence estimations based on drug use surveillance systems. Methods: Serial multi-method PDU/IDU prevalence estimations based upon capture-recapture, Poisson regression, multiplier and back-calculation methods. Comparative analysis of methods and assessment of their robustness to variations of external factors. Results: National PDU and IDU prevalence rates were estimated at 6.16/1,000 (95% CI 4.62/1,000 to 7.81/1,000) and 5.68/1,000 (95% CI 4.53/1,000 to 6.85/1,000) inhabitants aged 15–64 years, respectively. Absolute prevalence and prevalence rates of PDU increased between 1997 and 2000 and declined from 2003 onwards, whereas IDU absolute prevalence and prevalence rates witnessed an increasing trend between 1997 and 2007. Conclusions: Drug use surveillance systems can be valuable instruments for the estimation and trend analysis of drug misuse prevalence given multiple methods are applied that rely on serial and representative data from different sources and different settings, control multiple counts and build upon standardized and sustained data collection routines. The described institutional contact indicator revealed to be a useful tool in the context of PDU/IDU prevalence estimations and thus contributes to enhancing evidence-based drug policy planning.