In this nationwide study, 1975 students from grades 3, 6, and 9 (ages 9, 12, and 15 at the onset of the year), were recruited from randomly selected schools, which represented different geographical areas throughout Sweden. The main aim of the study was to assess the prevalence of self-reported pain (headache, abdominal, and musculoskeletal pain) and perceived health (problems sleeping and/or if they often felt tired, lonely and sad). A second aim was to study the co-occurrence among different pain and health variables. The students, (n = 1908 distributed by grade 3: 255 girls and 305 boys, grade 6: 347 girls and 352 boys, grade 9: 329 girls and 320 boys) answered retrospectively (three months) a specially designed questionnaire. Fifty percent (50%) of the students reported that they had experienced pain, either as headache, abdominal pain or musculoskeletal pain, within the recall period. Gender differences were especially noticeable for headaches, where twice as many girls (17%, n = 159) than boys (8%, n = 80) reported that they suffered such pain at least once a week or more often. Co-occurrence among the variables was moderate (0.3-0.5). For the total of the seven variables, the perception of pain and health complaints decreased with age for boys from grades 3 to 9, while multiple complaints increased for girls.