The structural protein-coding genomic regions of dengue virus type 1 (DEN-1) strains representing three distinct topotypes (Thailand, Philippines and Caribbean) were cloned and sequenced. In addition the envelope (E) nucleotide sequences of two recent Caribbean topotype DEN-1 isolates were obtained by direct RNA sequencing. The nucleotide sequence of the DEN-1 viruses in the structural gene region was found to be highly conserved with greater than 95% nucleotide sequence homology and with less than 4% change in the amino acid sequence. Although there was a less than 2% change in the nucleotide sequence of DEN-1 E proteins, strains could be differentiated by the clusters of nucleotide changes. Furthermore, the deduced amino acid changes in the E protein were clustered primarily within the proposed immunologically reactive regions. Genomic nucleotide sequence comparisons did not define geographical or virulence markers but located unique clusters of nucleotide/amino acid changes for each of the three topotypes of DEN-1 viruses examined.