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Background: Musculoskeletal disorders (MSDs) of the neck and shoulder are the most common and most influential factors causing disorder in the performance and absenteeism of work in administrative personnel. Aim: To identify risk factors which affect musculoskeletal disorders of neck and shoulder areas in headquarters staff of Kerman University of Medical Sciences. Methods: The present cross-sectional study was conducted in 2015 on 282 headquarters personnel of Kerman University of Medical Sciences (Kerman, Iran). The desired headquarters staff were selected from seven Deputy Vice-Chancellors of Kerman University of Medical Sciences, including Deputy of Health; Deputy of Treatment; Deputy of Education; Deputy of Students and Cultural Affairs; Deputy of Food and Drugs; Deputy of Management Development and Resource Planning; Deputy of Research and Technology, and data were gathered by using a standard Nordic musculoskeletal questionnaire NMQ (Nordic) and were analyzed by using SPSS version 16. The impact of various factors on the most common complications (neck and shoulder pains) was analyzed separately through logistic regression analysis and detailed Odds Ratio (OR) was calculated for each individual. Results: The occurrence of neck and shoulder pains in headquarters staff were 42.14% and 40.71%, respectively. In the prevalence of neck pain variables such as marital status (single than married p=0.01, OR=0.24), work experience (p=0.03, OR=1.07 ), education (bachelor’s degree and lower than master’s degree and higher p=0.003, OR=2.69), right / left-handedness (left than right p=0.03, OR=0.33), weight (p=0.04, OR=1.04), place of work (p |