Objectives: This study investigated whether playing wind instruments has adverse effects on musculoskeletal functions among junior high school students who play in music clubs. Material and Methods: The study included 210 junior high school students (35 boys, 175 girls) belonging to 1 of 4 different school clubs that practiced playing wind instruments more than 6 days/week. The mean age of the participants was 14 years. The study was performed using a questionnaire survey and an electromyographic examination of jaw and cervical muscle activities during playing wind instruments. Results: The prevalence of temporomandibular disorders (TMD) among the children playing woodwind (WW) or brass wind (BW) instruments was higher than in those playing non-wind (NW) instruments. Long duration of playing WW with a reed mouthpiece or BW with a small mouthpiece was suggested to affect the incidence of TMD, which was more marked in girls than in boys, irrespective of height or weight. Muscle activity in the masseter muscle during playing an instrument was significantly higher in the BW with a small mouthpiece group than in the NW group (p < 0.05). In cervical muscles, muscle activity of both the sternocleidomastoid and trapezius muscles was higher during playing BW than in the case of other instruments, and activity in the sternocleidomastoid muscle was significantly higher in the BW with a small mouthpiece group than in the case of other instrument groups (p < 0.05). Conclusions: Playing wind instruments may have adverse effects on musculoskeletal functions among junior high school students playing in music clubs as compared with playing NW instruments. The prevalence of TMD among the students playing wind instruments was higher than in those playing other instruments. Long duration of playing those instruments affects musculoskeletal function, and this effect is more marked in girls than in boys, irrespective of height or weight.