In an attempt to determine the types of non-polio enteroviruses (NPEVs) in acute flaccid paralysis (AFP) cases in Iran, we detected enterovirus 71 (EV71) in an AFP case with residual paralysis for the first time. Cell culture detected no enteroviruses, while RT-PCR and subsequent sequencing revealed that the specimen was positive for EV71. EV71 is the causative agent of a variety of diseases from hand, foot and mouth disease to severe neurological complications and is now considered as an important cause of childhood acute flaccid paralysis.