Two new studies report expression quantitative trait locus (eQTL) mapping of primary cells involved in innate immunity isolated from healthy humans. Julian Knight and colleagues report eQTL mapping of CD14+ monocytes from 432 healthy volunteers of European ancestry (Science 343, 2014, doi:10.1126/science.1246949). Monocytes were exposed to either interferon-γ or lipopolysaccharide (LPS) for a short (2-hour) or long (24-hour) duration. The majority of the cis eQTLs identified were specific to the condition tested. The authors also identified trans eQTLs and condition-specific gene networks. In a second study, Nir Hacohen and colleagues report eQTL mapping of dendritic cells isolated from the peripheral blood monocytes of 560 healthy individuals of European, Asian or African-American ancestry from the PhenoGenetic cohort (Science 343, 2014, doi:10.1126/science.1246980). They identified 264 cis eQTLs for resting dendritic cells. By stimulating dendritic cells with LPS, influenza virus or interferon-β, they identified 121 cis eQTLs for the response to 1 or more of the stimulation conditions, with 57 shared by all 3 conditions. The authors also identified trans eQTLs of IRF7. The two studies show overlap of eQTLs with loci that have previously been associated with particular autoimmune or infectious diseases and suggest further studies to explore disease mechanisms.