Abstract：Objective To compare the detection rate of enterovirus（EV）in swallow swab and fecal samples of patients with hand-foot-mouth disease, and to provide evidence for the monitoring sample selection of hand-foot-mouth disease. Method In 2013, 63 patients with hand-foot-mouth disease clinically diagnosed by medical institutions in Anshan district were collected and paired samples of pharyngeal swabs and feces were collected. Cox A16, EV 71 and other enter virus types were detected by real-time PCR. Results Among the 63 pairs of specimens, the positive rates of Cox A16, EV 71 and other Etiology in throat swabs were 26.98%, 1.59% and 31.75% respectively, and in excrements were 22.22%, 1.59% and 31.75% respectively. The results showed that the positive rate of viral nucleic acid in the two samples was not statistically significant（χ2＝0.534， P＞0.05）. The correlation between the two samples was statistically significant（χ2＝8.036， P＜0.05）. There was no significant difference in the positive rate of nucleic acid detection between the throat swab and the fecal paired sample（P＞0.05）. Conclusion The positive rate of nucleic acid detection in throat swab and fecal samples is the same, and throat swab samples can be taken instead of fecal specimens.