Injecting drug users are the principal at risk group for blood borne viruses. The aim was to assess the feasibility of screening substance misusers for blood borne viruses, and to offer appropriate vaccinations/referral to hepatology services. This was a nurse led prospective 6-month study based at a large Substance Misuse Service in south east England. Of the 196 consecutive individuals assessed, 81 were eligible for HBV immunization of whom only 33.3% completed a vaccination course. Prevalence of positive serological markers were: anti-HBc 14.4%, HBsAg 1.5%, and HCV antibody 37.9%. Compared to men, women were more likely to accept blood borne virus testing (83.3% vs. 62.3%), have ever injected (89.6% vs. 76.3%), overdose (54.2% vs. 23.6%), be anti-HBc positive (27.5% vs. 8.8%), drink alcohol above national recommended guidelines (41.7% vs. 25.7%), and have a positive HCV serology (55% vs. 30.4%) (P ≤ 0.05 for all). Of the 73 individuals identified with a positive HBsAg and or HCV antibody, only 14 (19.1%) were known to hepatology services and 8 (20%) of those eligible subsequently accepted a specialist referral. In conclusion, serological markers for blood borne viruses remain high in substance misusers (anti-HBc 14.4%, HCV antibody 37.9%), with women more likely to be positive. Overall, only 33.3% and 20%, respectively, complete HBV vaccination and accept a hepatology referral. A multidisciplinary approach is paramount to address both the blood borne viruses and the substance misuse and realignment of hepatitis services to Substance Misuse Services may offer such a strategy.