We have studied human rhinovirus (HRV) recovered from nasopharyngeal aspirates and middle ear fluids collected during acute otitis media with RT-PCR sequencing followed by phylogenetic analysis. In addition to a great diversity of traditional HRV types we found genetic relatives of the novel HRV species, suggested HRV-C, in both sample types. Our results indicate the presence of HRV-C in the middle ear for the first time.