Genetic polymorphism in the carnitine palmitoyl transferase 2 (CPT2) gene has been reported to be a susceptibility factor in a number of syndromes of acute encephalopathy with various infectious diseases, but evidence of its effect on enterovirus 71 (EV71) infection is lacking. The goal of this study was to examine the relationship between genetic polymorphism of CPT2 and severity of EV71 infection in a Chinese population. PCR of five exons of the CPT2 gene was carried out to identify single-nucleotide polymorphisms (SNPs) in EV71-infected subjects (n = 333), including mild cases (n = 271) and severe cases (n = 62) as well as healthy controls (n = 328). Blood ATP levels were measured within 24 h of admission. The frequency of the A allele of rs1799821 (P = 0.023) and the G allele of rs2229291 (P = 0.009) in the CPT2 gene was higher in patients with severe EV71 infection. The A-G haplotype of rs1799821and rs2229291 was directly linked to EV71 severe infection risk when compared to all other haplotypes (OR = 2.005, 95 % CI = 1.087-3.700, P = 0.024). The blood ATP levels of severe cases were significantly lower than in mild cases (P < 0.01) and controls (P < 0.01). A significant negative correlation was observed in haplotype A-G between ATP levels and physical findings in severe cases (P < 0.05). These findings suggest that CPT2 polymorphism may be associated with severity of EV71 infection and that the A-G haplotype of the CPT2 gene is involved in the inflammatory process of EV71 infection.