We investigated the causative agents of hand, foot and mouth disease (HFMD) in children in Beijing epidemic from April to June of 2007. Totally, 82 specimens (including throat swabs, rectal swabs and vesicular swabs) were collected from 51 patients with HFMD. All patients had typical skin lesions, but no neurological manifestations. These clinical specimens were directly tested by RT-PCR assay with three primer sets: universal enterovirus, CA16-specific and EV71-specific primers. Enterovirus, CA16 and EV71 were identified depending on the size of PCR products. The percentage of the specimens identified as positive for enterovirus was 70.6%. Of the 51 cases, 25 were positive for CA16, 4 were positive for EV71, and 7 were enterovirus positive of non-CA16 or EV71. The ratio among them was about 6:1:2. EV71 strains belonged to genotype C4 after sequencing and phylogenetic analysis.