Altshuler's academic research focused on human genetic variation and its application to disease,[10][11][12][13] using information from the Human Genome Project.[14] He has co-led the SNP Consortium, International HapMap Project,[15][16] and 1000 Genomes Project[17][18][19] His research focused on the genetic basis of Type 2 Diabetes, and his laboratory contributed to mapping dozens of gene variants that are associated with risk of Type 2 Diabetes, lipid levels, myocardial infarction, rheumatoid arthritis, lupus, prostate cancer, and other disorders.