Background Using a laptop for work is gaining rapid popularity, but there is little evidence how it influences the musculoskeletal disoders (MSD) and functional characteristics of the neck and shoulder area. The aim of this study was to compare the prevalence of MSDs and functional characteristics of the neck between office workers using a laptop or desktop computer. Methods A total of 110 office workers with a mean age of 41±10 participated. 45 office workers (73% female) were using a laptop and 65 office workers (86% female) a desktop computer. The prevalence of MSDs was recorded using the Nordic Musculoskeletal Questionnaire. Active range of motion (AROM), maximal voluntary isometric contraction (MVC) force, joint position error (JPE), and pain-pressure threshold (PPT) of the neck were measured. Results Laptop users had statistically significantly more MSDs in the right shoulder area on the day of participation (p<0.001, OR=4.47), during the previous 7 days (p<0.01, OR=3.74) and 6 months (p<0.01, OR=3.57). Laptop users had also significantly more left shoulder MSDs during the previous 7 days (p<0.05, OR=2.44). The prevalence of neck area MSDs was higher among laptop users, but not statistically significant. Desktop computer users had more MSDs in the low back during the previous 6 months (p<0.05, OR=2.24). There were no statistically significant differences in any of the functional characteristics of the neck between the groups. Conclusions Using the laptop computer for work can cause a higher chance of developing MSDs in the neck and shoulder area, but might not have a long-term effect on the functional characteristics of the neck.