Received: September 2013, Accepted: March 2014 Background: Today application of computer in the life of people is very common and those who work with computer in especially long -term are faced with musculoskeletal pains. The aim of this study was to investigate risk factors of musculoskeletal and Joint pains among computer users in Rafsanjan city in the years 2012-13. Materials and Methods: In this descriptive study, 420 computer users were recruited in Rafsanjan city between 18 April 2012 and 19 January 2013. The data were collected by a checklist, in face to face interview sessions. Data were analyzed in SPSS and parametric and nonparametric tests were used where appropriate. Results: Cervical pain was associated with position of desk, chair and keyboard. There were significant association between shoulder pain and position of the keyboard, low back pain and chair position, carpal tunnel syndrome and mouse usage. The prevalence of cervical pain, shoulder pain, arm pain, wrist pain, hand pain, low back pain, elbow pain, back pain, and carpal tunnel syndrome, among respondents were 38.3%, 38.3%, 27.1%, 21.2%, 18.8%, 24.5%, 15.7%, 26.4% and 21.2%, respectively. In this study, there was significant association between exercise and all variables of carpal tunnel syndrome, elbow pain, back pain, low back pain and shoulder pain. Conclusions: It can be concluded that prevalence of musculoskeletal pain in computer users in our study were very common. Improving the position of desk, chair, mouse and keyboard could help with reducing cervical pain, shoulder pain, back pain, low back pain and carpal tunnel syndrome.