BACKGROUND: The Patient Health Questionnaire (PHQ-9) and the Generalized Anxiety Disorder scale (GAD-7) are widely used symptom-based instruments for screening depression and anxiety. However, their validation in Chinese children and adolescents remains insufficient. We aim to investigate the performance and optimal cut-offs of PHQ-9 and GAD-7 in Chinese children and adolescents in screening clinical depression and anxiety, and to discuss the influencing factors of the cut-offs. METHODS: The study subjects were chosen from 3 sites of the Mental Health Survey for Children and Adolescents in Yunnan (MHSCAY), a total of 2,237 participants who had been screened positive by self-administered questionnaire and further diagnosed by using the gold standard were included in the final analysis. The Receiver Operating Characteristic (ROC) curves were used to determine the discriminative ability of the two instruments, measured by using the area under curve (AUC). The optimal cut-offs of the two instruments were determined by the maximum Youden's index. A series of stratified analyses were performed to discover the best cut-offs for children and adolescents of different characteristics. Logistic regression models were adopted to evaluate the influence of self-harm (SH) on identified optimal cut-offs. RESULTS: We found the performance was generally poor for both the PHQ-9 and GAD-7 in screening clinical depression and anxiety in our study sample, with the AUCs ranged only between 0.622-0.712. When using the two instruments for diagnosis purpose, 11 was the optimal cut-off for both clinical depression and anxiety (AUC for PHQ-9: 0.664, AUC for GAD-7: 0.669). For study subjects of different age, gender, race, and left-behind status, discordant cut-offs were identified. SH also showed conspicuous influence on the optimal cut-offs of PHQ-9 and GAD-7, and the combination of SH information can increase screening accuracy of PHQ-9 in some subgroups. CONCLUSIONS: Both the PHQ-9 and GAD-7 showed poor performance in screening clinical depression and anxiety in our study sample. This crucial finding suggests that, despite the wide use of the two scales, they might be fundamentally inadequate for depression and anxiety screening in Chinese children and adolescents. Other screening tools of higher accuracy should be developed and used in this age group.