[1] Davenport's first faculty position was as a professor of zoology at Harvard, where he became one of the most prominent American biologists of his time, pioneering new quantitative standards of taxonomy.

During his time at Cold Spring Harbor Laboratory, Davenport began a series of investigations into aspects of the inheritance of human personality and mental traits, and over the years he generated hundreds of papers and several books on the genetics of alcoholism, pellagra (later shown to be due to a vitamin deficiency), criminality, feeblemindedness, tendency to seafaring, bad temper, intelligence, manic depression, and the biological effects of race crossing.

Although he was one of the first scientists to recognize polygenic inheritance (the influence of many genes on a single trait), he continued to employ simple Mendelian models when convenient for making racist and classist claims.

He and his assistants turned repeatedly to Jamaica as a laboratory for studying the heredity of physiological and intellectual characteristics due to its large mixed-race population.

Davenport aspired to found a World Institute for Miscegenations, and "was working on a 'world map' of the 'mixed-race areas,[16] which he introduced for the first time at a meeting of the IFEO in Munich in 1928.

The results of their research was presented in the book Race Crossing in Jamaica (1929), which attempted to provide statistical evidence for biological and cultural degradation following interbreeding between white and black populations.

[18] Particularly caustic was the review of the book published by Karl Pearson at Nature, where he considered that "the only thing that is apparent in the whole of this lengthy treatise is that the samples are too small and drawn from too heterogeneous a population to provide any trustworthy conclusions at all".

Sharing the racist views of many scientists during this time, those that Davenport considered to be genetically inferior included Black people and Southeastern Europeans.

[20] In all, Davenport’s efforts served to provide scientific justification to social policies he supported, and immigration was one way this manifested in the beginning of the 20th century.

He held editorial positions at two influential German journals, both of which were founded in 1935, and in 1939 he wrote a contribution to the Festschrift for Otto Reche, who became an important figure in the plan to "remove" those populations considered "inferior" in eastern Germany.

[21] In a 1938 Letter to the Editor of Life magazine, he included both Franklin Roosevelt and Joseph Goebbels as examples of crippled statesmen who, motivated by their physical defects, have "led revolutions and aspired to dictatorships while burdening their country with heavy taxes and reducing its finances to chaos.

Six years after he retired in 1934, Davenport held firm to these beliefs even after the Carnegie Institute pulled funding from the eugenics program at Cold Spring Harbor in 1940.