Medical waste handlers (MWHs) are at risk of exposure to serious viral infections. No data are available on the prevalence of hepatitis B virus (HBV), hepatitis C virus (HCV) or human immunodeficiency virus (HIV) among MWHs in Libya. During a one-year period (January to December 2004) blood samples from 300 (59 females) MWHs employed by a local contractor in Tripoli and 300 blood samples from non-medical waste handlers (NMWHs) who had no direct or indirect contact with medical waste were examined for HBV, HCV and HIV using enzyme-linked immunosorbent assays. HBV was detected in 7 (2.3%) and 1 (0.3%) and HCV in 8 (2.7%) and 0 (0.0%) of MWHs and NMWHs, respectively. Significant differences were observed in the detection rates of HBV (OR: 7.14; P<0.04) and HCV (OR: undefined; P<0.005) in MWHs when compared with NMWHs. HIV was not detected in both groups. Of the MWHs studied, 21% were immunised against HBV and 7% were trained to handle medical waste. In addition, 99.7% wore overalls, 57.7% thick disposable gloves, 55% boots and 17.7% masks while handling medical waste. In conclusion, prevalence rates of HBV and HCV were significantly higher in MWHs than those in NMWHs examined. Training, immunisation, and post-exposure protection of MWHs, in addition to proper management of medical waste by the health authorities, may significantly reduce the risk of acquiring infectious agents by MWHs in Libya.