Dr. Cairns was the Director of CSHL from 1963-1968. This was a time of institutional friction and unrest which led to the Department of Genetics being given over to the Bio Lab and then the founding of CSHL Quantitative Biology, which eventually was shortened to CSHL in 1963. The combined entities were in dire financial straights with a grim outlook for survival.

Dr. Cairns forecasted it would take $750,000 to renovate the labs and residences to make CSHL a world class facility. He tapped into revenues from the increasingly lucrative Symposia to finance the building costs. Dr. Cairns also brought in new talent: Cedric Davern from Australia and Joseph Speyer from NYU. Both Davern and Speyer had grants to cover research and Cairns’ own salary was covered by a grant for five years - evidence of Cairn’s adroit financial maneuverings. Meanwhile, Dr. Cairns continued his own research in Demerec Lab. The research by Cairns, Speyer, and Davern shifted the Lab’s focus to DNA and laid the platform for James D. Watson to assume directorship in 1968.

However, CSHL was not yet out of the woods. Due to financial concerns regarding the future of CSHL, Davern and Speyer left for academic positions. Cairns weathered friction with Edward Tatum, the chair of CSHLQB, an absentee board, and loss of local community support before finally waving his white flag and resigning in 1968.

Dr. Watson continued to support Dr. Cairns and his research and secured funds from the American Cancer Society to allow Dr. Cairns to stay on at CSHL as professor from 1968-1972. Dr. Cairns then left CSHL for Mill Hill Laboratory, Oxford, England.