He is best known for his work in Florida, Havana and at the Panama Canal in abating the transmission of yellow fever and malaria by controlling the mosquitoes that carry these diseases, for which he used the discoveries made by the Cuban doctor Carlos J. Finlay.

[4] In 1898, after the end of the Spanish–American War, Gorgas was appointed Chief Sanitary Officer in Havana, where he and Robert Ernest Noble worked to eradicate yellow fever and malaria.

Through his efforts draining both the Aedes aegypti mosquito vector breeding ponds and quarantining of yellow fever patients in screened service rooms, cases in Havana plunged from 784 to zero within a year.

These measures were instrumental in permitting the construction of the Panama Canal, as they significantly prevented illness due to yellow fever and malaria (which had also been shown to be transmitted by mosquitoes in 1898) among the thousands of workers involved in the building project.

That same year, Gorgas and George Washington Goethals were awarded the inaugural Public Welfare Medal from the National Academy of Sciences.