The present paper aimed to analyze the correlation between estradiol and cytokines in the patients with severe hand, foot and mouth disease (HFMD), and to provide information for the diagnosis and treatment of this disease. The samples of children with clinically diagnosed HFMD were collected. Enterovirus 71 (EV71) and other enteroviruses were detected by fluorescent quantitative reverse transcription-polymerase chain reaction (RT-PCR). The serum estradiol and cytokines were detected by chemiluminescent immunoassay and Milliplex xMAP assays respectively. The results showed that the concentrations of estradiol in severe HFMD, mild HFMD and healthy control groups were (6.12±6.08) pg/mL, (30.2±10.16) pg/mL and (20.62±7.43) pg/mL, respectively. There were significant differences in the concentrations of interferon γ (IFN-γ), interleukin 8 (IL-8) and IL-6 between severe HFMD group and mild HFMD group. Serum IL-8 and IL-6 levels were negatively correlated with estradiol concentration. The results suggest that serum estradiol concentration in HFMD patients is closely related to IFN-γ， IL-8 and IL-6 levels, which could be used as a biomarker for clinical judgement of severe HFMD.