BackgroundHand, foot, and mouth disease (HFMD) caused by enterovirus 71 (EV71) is a potentially life-threatening infectious disease that commonly occurs in children. Diagnosis of HFMD caused by EV71 largely depends on clinical manifestations and rare serological biomarkers used to identify children suffering from HFMD. Serum cholinesterase (SChE) activity has frequently been reported as a potential biomarker for solid central nervous system tumors, chronic heart failure, and liver cirrhosis. However, its potential value in the diagnosis of neurotropic virus infections, such as HFMD caused by EV71, remains to be determined.FindingsIn our study, 220 children hospitalized with HFMD caused by EV71, 34 inpatients infected with coxsackievirus A16 (CVA16), and 43 undefined enterovirus-infected HFMD inpatients were recruited at the Anhui Provincial Children’s Hospital between January 2011 and December 2012. SChE activity was measured. The non-parametric Mann–Whitney U test showed that SChE activity in children diagnosed with HFMD caused by EV71 was significantly higher than in healthy controls (p < 0.001), as well as in children with upper respiratory tract infections (p = 0.011), bronchopneumonia (p < 0.001), septicemia (p < 0.001), amygdalitis (p < 0.001), and appendicitis (p < 0.001). In addition, higher SChE activity was observed in male inpatients with HFMD caused by EV71 (47.7 % positivity) compared to female inpatients (26.1 % positivity) (chi-square test, p = 0.002). In our study, no significant differences in SChE levels were observed among different ages (up to 120 months) (r = -0.112, p > 0.05). An important finding was that SChE activity declined in the recovery phase of HFMD caused by EV71 compared to the acute phase (p < 0.001).ConclusionsElevated SChE activity was observed in patients with severe HFMD caused by EV71. Therefore, SChE might be a potential assistant biomarker for the diagnosis of HFMD caused by EV71 in children.Electronic supplementary materialThe online version of this article (doi:10.1186/s40249-016-0124-y) contains supplementary material, which is available to authorized users.