The purpose of this study was to evaluate self-rated musculoskeletal complaints and their association with computer use time in the adolescent population in Lithuania. The cross-sectional study done in 2008–2009 in Lithuania. 1806 students aged 13–18 years from randomly selected schools were questioned (response rate 95.8%). Logistic regression analysis results show that musculoskeletal complaints in adolescence are associated with duration of computer use as related to age and gender. Compared with adolescents using computer <2 hours daily, a statistically significant probability of experiencing back pain was determined for younger boys and girls groups (13–15 years) who reported working on a computer >4 hours (OR=2.36 and OR=2.50, respectively) in older age groups (16–18 years); in girls only the ORs of back pain significantly increased with increased time of computer use. the probability of experiencing the neck-shoulder pain was determined only in girls aged 16–18 years who reported working on a computer 2–4 hours (OR=1.62, p=0.020). Musculoskeletal complaints in adolescence are related to duration of computer use. Increasing the time spent at the computer increased complaints of musculoskeletal pain among Lithuanian adolescents. The main guidelines for prevention point to restriction of time of computer use.