Objective: To investigate knowledge and behaviors towards infectious diseases and factors associated with school absence for health reasons among primary and middle school students across 10 provinces in China, and to provide a reference for conducting a targeted health education of infectious disease and improving the controling and preventing levels of infectious disease in schools. Methods: Stratified multistage sampling was used in this self-administered, anonymous questionnaire survey was conducted among 17 042 primary and middle school students across 10 provinces during Mar. to Dec. 2013. Multivariate Logistic regression models were performed to identify factors associated with school absence for health reasons. Results: About 57.1% of all the participants reported infectious disease-related symptoms including fever, cough, headache, abdominal pain, diarrhea, as well as rash during the past two weeks; 42.4% reported absence from school for health reasons during the past year. The awareness rate of infectious diseases was between 42.5%-87.8%, and reported rates of behaviors towards infectious disease prevention were between 28.8%-97.7%. Living with parents(OR=0.91, 95%CI=0.84-0.99), higher father’s education level(OR=0.88, 95%CI=0.81-0.95), higher mother’s education level(OR=0.85, 95%CI=0.79-0.92), adequate knowledge and behavior towards infectious disease prevention (OR=0.97, 95%CI=0.96-0.98) and living in eastern areas (OR=0.90, 95%CI=0.83-0.98) were significantly associated with school absence for health reasons during the past year. Conclusion Knowledge and behaviors towards infectious diseases among primary and secondary school remains to be improved. Education on infectious disease prevention should be strengthened in schools to prevent the transmission and prevalence of infectious diseases.