Abstract: Objective To investigate the clinical significance and the change of immune function in HFMD infected by CoxA16 virus by measuring the expression of T lymphocyte subtype, Interleukin-4 and Interleukin-6 in children with HFMD. Methods 61 cases of CoxA16-positive proved by Real-time fluorescent PCR detecting the throat swabs were recruited from Apr 2013 to Sep 2014.The peripheral blood of all patients were collected in acute stage and convalescent stage, serving healthy children as control. T lymphocyte subtype was determined with FCM. ELISA was used to examine Interleukin-4 and Interleukin-6. Results The rate of T lymphocyte subtype CD3+, CD4+ and CD4+/CD8+ in acute stage were lower, while CD8+ increased comparable to those of convalescent stage and the control group (tCD3+=4.217, 4.978；tCD4+=4.196, 5.103；tCD4+ /CD8+=3.326, 3.894；tCD8+=4.018, 4.325, P＜0.05). IL-4 in acute stage decrease remarkably comparing with convalescent stage and the control group. However, IL-6 in acute stage was significantly higher comparing with convalescent stage and the control group（tIL-4=5.824,6.213；tIL-6=6.352,7.195,P＜0.05）. Conclusion There are function disorders of cellular immune function in children infected by CoxA16 virus, which might be related to pathopoiesia mechanism.