In January 1998, dengue-3 (DEN)-3 (group III genotype) was detected in Puerto Rico after an absence of 20 years. Public health officials intensified education efforts to promote community participation in dengue control. Virologic surveillance revealed an unexpected paradox: DEN-4 and DEN-1 produced a large epidemic overlaying the DEN-3 epidemic. In 1998 there were 17,000 reported cases of dengue (4.8/1,000 persons), and among all virus isolations (n = 960), DEN-4 (419, 43.6%), DEN-1 (337, 35.1%), and DEN-2 (143, 14.9%) were detected much more frequently than DEN-3 (61, 6%). Age group-specific attack rates were highest for persons 10-19 years old, followed by infants less than a year of age. Nineteen fatal cases (median = 37 years old, range = 8 months to 90 years) had a positive laboratory diagnosis of dengue. Among DEN-3 cases no fatalities were documented, 50 were hospitalized, and 10 of 48 (21%) fulfilled the criteria for dengue hemorrhagic fever (four had primary infections and six had secondary infections). During 1999, DEN-3 became the predominant serotype isolated (182 of 310 isolations, 59%). The reappearance of DEN-3 and its subsequent circulation from 1999 to 2001 produced no changes in dengue incidence that could have been detected in the absence of virologic surveillance.