Professor Deacon's research has combined human evolutionary biology and neuroscience, with the aim of investigating the evolution of human cognition. His work extends from laboratory-based cellular-molecular neurobiology to the study of semiotic processes underlying animal and human communication, especially language. Many of these interests are explored in his 1997 book, The Symbolic Species: The Coevolution of Language and the Brain.
His neurobiological research is focused on determining the nature of the human divergence from typical primate brain anatomy, the cellular-molecular mechanisms producing this difference, and the correlations between these anatomical differences and special human cognitive abilities, particularly language. In pursuit of these questions he has used a variety of laboratory approaches including the tracing of axonal connections, quantitative analysis of regions of different species brains, and cross-species fetal neural transplantation. The goal is to identify elements of the developmental genetic mechanisms that distinguish human brains from other ape brains, to aid the study of the cognitive consequences of human brain evolution.