The present paper aims to analyze the etiological and molecular characteristics of enterovirus (EV) in acute respiratory infections in shanghai, China between 2009 and 2011. Nasopharyngeal swabs were obtained from 2 282 patients with acute respiratory tract infection (ARTI) complications in three sentinel hospitals in Shanghai. Enteroviruses were screened by multiplex polymerase chain reaction (PCR) using RV15 kit. Then the serotypes of enterovirus were determined by semi-nested reverse transcriptase (RT)-PCR. The results demonstrated that 34 (1.49%) were positive for enterovirus. Among them, coxsackievirus A2 (CVA2) (17.6%), CVB5 (17.6%) and CVA5 (14.7%) were most frequently detected. But rare enterovirus serotype (EV68 and CVA21) were detected. According to the N-J phylogenetic tree, the Shanghai CVA2 isolates shared high similarity (98.1%) with one Beijing isolate in 2009; the Shanghai CVA5 isolates shared high similarity (99.7%) with the mainland China strains from 2007 to 2009; the Shanghai CVB5 isolates shared high similarity (99.7%) with the mainland China strains in 2009; the Shanghai CVA21 isolates shared high similarity (99.4%) with the mainland China strains from 2002 to 2008; the Shanghai EV68 isolates shared high similarity (96.6%) with the mainland China strains from 2006 to 2008. It is concluded that CVA2, CVB5 and CVA5 are most frequently detected in acute respiratory infections in Shanghai, China between 2009 and 2011. Phylogenetic analyses showed that the Shanghai isolates are closely related to the mainland isolates before 2009.