Hexon sequences were analyzed in 29 epidemiologically unrelated adenovirus type 3 (Ad3) isolates from the 7 genome types to understand the molecular basis of the genome-type diversity of Ad3 associated with childhood pneumonia in Korea during the period 1991-1999. Nine nucleotide substitutions were observed among the 29 Ad3 strains. Five of the 9 involved amino acid changes in loops 1 (Gly to Val at codon 205 and Thr to Ile at 211) and loop 2 (His to Asn at 417, Thr to Ala at 429, and Ala to Asp at 439). The predicted hydropathic characteristics of this region have been affected by these amino acid changes. The region surrounding codons from 417 to 439 of Ad3a16 and Ad3a18 manifested greater hydrophobicity than the region of other genome types (Ad3a, Ad3a13, Ad3a14, Ad3a15, and Ad3a17). In particular, three amino acid changes in loop 2 were associated with two new genome types, namely, Ad3a16 and Ad3a18, which were recognized during later epidemics in 1998-1999. Phylogenetic relatedness revealed that these two genome types clustered into distinct lineages in the phylogenetic tree. This result suggests that the genetic heterogeneity of Ad3 hexon could play a potential role in the appearance of new genome types and that it could affect the antigenic characteristics of Ad3.