Reporting of percutaneous injuries (PIs) to the Chinese Exposure Prevention Information Network (EPINet) became mandatory for all public and tertiary referral hospitals in Taiwan in 2011. We have estimated the number of microbially contaminated PIs and the national PI incidence using a retrospective secondary data analysis approach to analyse 2011 data from the Chinese EPINet to determine the types of PI, mechanisms of occurrence and associated risks. The results revealed a national estimate of PIs between 6710 and 8319 in 2011. The most common incidents for physicians were disposable syringes, suture needles, and disposable scalpels; while for nurses they were disposable syringes, intravenous catheters, and lancets. About 13·0% of the source patients were seropositive for hepatitis B virus (HBV) surface antigen, 13·8% were seropositive for hepatitis C virus (HCV), and 1·1% seropositive for human immunodeficiency virus (HIV). From these results we estimate that annually 970 full-time healthcare workers (HCWs) would be exposed to HBV, 1094 to HCV, and 99 to HIV. This study improves our understanding of the mechanisms and risks of PIs and informs the development of more efficient preventive measures to protect HCWs from such injuries.