The aim of this longitudinal study was to assess changes with age regarding prevalence of pain and perceived health in a student population, as well as change over time at grade level. Pain included frequency of headache, abdominal, and musculoskeletal pain and perceived health included problems sleeping and/or if they often felt tired, lonely, and sad. If gender, age (grade level), stress, physically activity were related to pain and health complaints were tested with multivariate logistic regression analysis. The students (n = 1908) came from randomly selected schools throughout Sweden and attended grades 3, 6 and 9 (ages 9, 12 and 15 at the onset of the year) in 2001. Three years later, 67% (n = 1276) of the same students answered a questionnaire that was constructed for the purpose of the studies. The responses given by the same students showed that girls’ complaints of pain and perceived health increased with age and boys decreased. Over half (56%) of the girls and two-thirds (67%) of the boys reported no frequent complaints either year. At grade level most variables were rated the same as three years earlier by the same age group. Stress was significantly related to pain and health complaints for girls and the risk of complaints, as calculated with odds ratio, was most evident for students who were characterized as being physically inactive in 2001 and remained inactive three years later. Jointly, significant predictors, such as stress, being physically inactive, gender and grade level, explained 8–20% of the frequent complaints.