Human metapneumovirus (hMPV) was identified in 2001 as a cause of acute respiratory illness, but its characteristics are still being defined. We analyzed 3740 nasopharyngeal-wash specimens obtained during 2002-2004, using assays for common respiratory viruses and real-time polymerase chain reaction for hMPV. We detected hMPV in 5% of all specimens, compared with 28% for other respiratory viruses. Nucleotide sequence analysis of hMPV isolates revealed the predominant circulation of hMPV genotype A in the 2003 season but a switch to predominantly genotype B in 2004. Sequence analysis also revealed major differences in the hMPV G and SH genes but relative conservation of the F and N genes within each genotype. Phylogenetic analysis indicated a seasonal switch within hMPV genotype A subtypes as well. Despite genetic variability, we found no difference in the severity of illness caused by various hMPV isolates. These findings suggest that hMPV may vary in genetic structure, to allow for a seasonal shift in predominant genotype and the maintenance of infection rates.