Human parechoviruses (HpEVs) are small icosahedral viruses, which cause a spectrum of debilitating illnesses in infants including cardiomyopathy and encephalitis. A basic building block of their virion is composed of three proteins referred to as VP-1, VP-3, and VP-0, which assemble into pentameric assemblies, where by 12 pentamers make up the virion. For decades, HpEVs were considered to be closely related to human enteroviruses due to similarities in the disease etiology they cause. We solved a crystal structure of HpEV-1, to 3.1Å resolution, which demonstrates that HpEVs are different from enteroviruses. HpEV-1 lacks a capsid surface structural feature known as the canyon, which is a site of receptor binding in many enteroviruses. Moreover, a cavity of VP1, which is normally occupied by a pocket factor in enteroviruses is completely filled with bulky hydrophobic residues in HpEVs. Furthermore, the N-terminus of V-P0 of HpEV-1 appears to have undergone 3D dimensional domain swapping, which results in inter-pentamer connectivity not seen in enteroviruses. HpEVs virion is smaller than any enteroviruses characterized to date. Internal surface of HpEV-1 is negatively charged around the five-fold axis of the pentamer and this is where a stretch of icosahedrally-ordered RNA was found to reside. RNA bases were found to stack against a highly conserved tryptophan-21 residue of VP-3 protein. Mapping sequence differences of various parechovirus serotypes onto the structure of HpEV-1, demonstrated that serotype-specific differences tend to reside on the surface of the virion. Fitting the crystal structure of the virion into the previously determined tomographic reconstruction of HpEV-1-receptor complex revealed that receptor binding occurs close to the 5-fold symmetry axis. Unexpectedly, the structure also demonstrated that the major antigenic-site of HpEV-1 is found on the inside of the virion. Structure-based phylogenetic analysis established that HpEVs are closer related to human hepatitis A virus than to any known enterovirus. In summary, our work provides structural framework for further understanding the life cycle of human parechoviruses and for the development of novel anti-viral therapeutics against this class of human pathogens.