His work focused on saturation mutagenesis as well as the developmental genetics of the Zeste- White region of the Drosophila X Chromosome.
During this time, Kaufman began his collaboration with Rob Denell that focused on a set of mutations that caused dominant defects in the fly’s head and anterior thorax.
[7] In his personal statement for the National Academy of Sciences he states that "The goal of my laboratory is to contribute to an understanding of the genetic regulation development of higher organisms.
The role of the Hox genes is best viewed as a set of developmental switches for decisions of segmental fate.
The encoded homeodomain has shown that this switch activity is carried out through the transcriptional regulation of target genes.
"[4] He has expanded his research from Drosophila to include several other insects and members of other subphylums under the phylum Arthopoda, such as Crustacea, Chelicerata and Myriapoda.