Epidemiologic studies conducted in the 1990s identified several independent healthcare associated risk factors for HBV and HCV infections in Pakistan. In 2002, we re-examined healthcare associated HBV and/or HCV infection risk factors in volunteer blood donors. In this case-control study, we collected data using a structured questionnaire on socioeconomic attributes, putative healthcare related risk factors, and other known factors for HBV and HCV infections in Karachi, Pakistan. The multivariable logistic-regression model (166 cases, 394 controls) after adjusting for socio-demographic attributes and other known HBV and HCV risk factors revealed that more cases than controls had multiple lifetime hospitalization, adjusted odds ratio (AOR) = 2.48; 95% confidence interval (CI) 1.04, 5.94, and had received dental treatment from an unqualified provider (AOR = 5.90, CI, 1.66, 21.02). More cases than controls had received a large number of therapeutic injections during the last 5 years (1-5 injections vs. 0, AOR = 2.64, 95% CI 1.06, 6.60; 6-19 injections vs. 0, AOR = 4.09, 95% CI 1.59, 10.51; > or = 20 injections vs. 0, AOR = 4.34, 95% CI 1.70,11.07), and had their last injection given using a re-usable glass syringe (AOR = 3.41 CI 1.13, 10.29). Our data suggest that risk factors for HBV and HCV infections identified in the last decade have remained unchanged in healthcare facilities in Karachi. Additional multi-disciplinary efforts are needed to control healthcare associated HBV and HCV transmission in Pakistan.