Abstract: Objective To study and compare the pathogen characteristics of patients with herpes stomatitis and herpangina. Methods From March 1,2015 to August 31,2015,60 cases diagnosed clinically as herpetic stomatitis and 50 cases as herpangina were included in this study.Colloidal gold assay was used for the detection of two kinds enterovirus of CoxA16 and EV71,ELISA was used for the detection of herpes virus Ⅰ and Ⅱ,RT-PCR method was used for the detection of enterovirus 5'-UTR gene fragment,EV71 VP1 and CoxA16 VP1 sequence,PCR was used for the detection of herpes virus Ⅰ and Ⅱ glycoprotein gene sequences.The pathogen differences of the two diseases were compared. Results For patients with Herpes stomatitis,PCR results showed the positive herpes virus in 38 cases,positive intestinal virus in 18 cases,not clear pathogen in 4 cases;IgM results showed positive herpes virus in 35 cases,positive intestinal virus in 11 cases.For Herpangina,PCR results showed positive herpes simplex virus in 2 cases,positive intestinal virus in 38 cases;IgM results showed positive herpes virus in 2 cases,positive intestinal virus in 35 cases.In the cases diagnosed clinically as herpetic stomatitis and herpangina cases,some pathogenic results were intersectional. Conclusion There may be some confusion between the clinical diagnosis of herpes stomatitis and herpangina,the pathogen can be rapidly determined by ELISA and colloidal gold method,and the PCR detection method can be further carried in some cases that is difficult to identify.