Neck/shoulder pain (NSP) is a common problem for adolescents and posture has been suggested as an important risk factor. The aim of this cross sectional study was to examine the relationship between prolonged NSP and habitual sitting posture in adolescents. The habitual sitting postures of 1593, 14-year-old adolescents with and without prolonged NSP were assessed using sagittal plane digital photographs. Cervicothoracic and lumbopelvic posture angles were calculated from the digital images using motion analysis software. Adolescents reported experience of NSP by questionnaire. Differences between postures of males and females and those with and without prolonged NSP were examined using independent t-tests. The relationships between cervicothoracic and lumbopelvic postures and presence of prolonged NSP were investigated using logistic regression models controlling for gender. Prolonged NSP was reported by 5.3% of the adolescents, with females reporting a higher prevalence rate (6.5%) than males (4.2%). Females also sat more erect with a more lordotic lumbar posture than males. Adolescents with prolonged NSP had more flexed cervicothoracic posture, more erect trunk and more lumbar lordosis. When gender was controlled, only lumbar lordosis was related to the presence of prolonged NSP.