Major depressive disorder (MDD), dysthymia disorder (DD) and bipolar disorder (BD) are the most prevalent affective disorders. A nationwide epidemiological investigation of MDD, DD and BP in school-attending children and adolescents was carried out, taking the effect of age, gender and comorbidity into consideration.A two-stage nationwide epidemiological study of point prevalence was conducted. Using a multistage cluster stratified random sampling strategy. The sample distribution was described, and the point prevalence of affective disorders was estimated. Chi-squared tests were used to compare disease prevalence based on sex and age. Comorbid ratios for MDD, DD and BP were calculated.The total number of cases in Stage 1 was 72,107 (aged 6-16 years). The point prevalence of MDD, DD and BP were 2.004 % (95 % CI: 1.902 to 2.106), 0.352 % (95 % CI: 0.309 to 0.395) and 0.856 % (95 % CI: 0.788 to 0.923), respectively. The total prevalence of affective disorder was 3.212 % (95 % CI: 3.079 to 3.338). The total prevalence of affective disorders between sexes (female: 3.834 % versus male: 2.587 %, χ2 = 90.155, p < 0.001) was consistent with the gender difference in MDD, DD and MD. The total prevalence of affective disorders in adolescents was higher than that in children (adolescents: 5.024 % versus children: 1.863 %, χ2 = 566.841, p < 0.001).Our study is the first nationwide survey on the prevalence of affective disorders among school-attending children and adolescents aged 6-16 in China. Our results also highlighted the importance of addressing comorbidities in future studies of affective disorders.