Enterovirus 71 (EV71) infection mainly causes hand-foot-mouth disease (HFMD) in infants and young children. There are many commensal bacteria in the environment of viral infection. It was reported that lipopolysaccharide (LPS) plays an important role in some enterovirus infections. This study aims to investigate the effects of LPS on EV71 infection. EV71 was co-incubated with LPS to determine its impact on the viral viability and infectivity. Results showed that LPS-incubated EV71 lost their viability slower than that of the EV71 control in a LPS concentration-dependent manner. In contrast, the infectivity of EV71 decreased when the virus was pretreated by LPS. The immunoblotting assay showed that LPS could bind with EV71 competitively with anti-VP1. EV71 from HFMD patients can be detected by anti-E.coli antibodies. The observations indicated that LPS can increase the thermal stability of EV71 and inhibit viral infection. Both effects might be ascribed to the capability of LPS binding with the virus.