The nucleotide sequence of the 240 bp E/NS1 junction of 81 dengue viruses isolated from cases in Jeddah, Saudi Arabia was determined and used to serotype the viruses. The nucleotide sequences of the complete Envelope (E) genes of 19 isolates were used for a phylogenetic analysis of the dengue viruses circulating in Saudi Arabia from 1994 to 2006. Three of the four dengue serotypes (DENV-1, DENV-2 and DENV-3) were found to circulate, often with more than one serotype in each outbreak. There was a major outbreak caused by DENV-1 and DENV-2 in 1994 while DENV-3 emerged in 1997. In the summer of 2004, all three serotypes were isolated and this gave way to an extended outbreak of DENV-1 that stretched from the summer of 2005 through early 2006. In the 1994 outbreak, the DENV-1 circulating was from the America-Africa genotype (lineage India-2) while the most recent outbreak in 2005 and 2006 was caused by a different DENV-1 strain from genotype Asia (lineage Asia-2), suggesting a re-introduction of DENV-1 a decade after the first introduction in 1994. There has been no change in the genotypes of DENV-2 (cosmopolitan genotype) and DENV-3 (genotype III) circulating since introduction in 1994 and 1997, respectively.