Although musculoskeletal problems are commonly reported among the working population, including nurses, the prevalence and risk factors for musculoskeletal discomfort in nurses have not been extensively studied in Taiwan. To understand the risk factors and prevalence of musculoskeletal discomfort in different body parts among nurses in Taiwan, we performed a cross-sectional study using a self-administered questionnaire to collect data. A total of 5,269 (93%) nurses completed the questionnaire survey. Musculoskeletal discomfort was found to be prevalent in this group. In terms of location, the lower back was the most commonly reported site of discomfort, followed by lower legs, shoulders and neck. Considering limitation of motion as an indicator of musculoskeletal discomfort severity, the highest levels of prevalence were reported, respectively, in the lower back, shoulder, lower leg, and wrist. Numbness was most commonly reported in lower legs, hands, thighs, and lower back. Risk factors for pain in shoulders/neck included waist-bending and waist-twisting, while those for lower back pain included duration of standing, waist-bending, and weight-lifting. Risk factors for lower leg pain included duration of standing and weight-lifting. Musculoskeletal discomfort was prevalent among nurses (91.6%). Pain in different body parts was related to different ergonomic risk factors while at work, namely, bending and twisting of the waist, and standing for extended periods of time. The development and testing of interventions to minimize these risk factors is warranted in future studies.