Immortalized human lymphoblastoid cell lines have been used to identify genetic factors affecting differential sensitivities in response to drug treatment. Our objective is to extend the application of such studies to investigative toxicology by assessing inter-individual and population-wide variability and heritability of chemical-induced toxicity phenotypes using cell lines from the Centre d'Etude du Polymorphisme Humain (CEPH) trios assembled by the HapMap Consortium. Cell lines from the CEPH trios were exposed to three concentrations of 14 environmental chemicals and two cellular toxicity response endpoints were assessed. We show that variability of response across the cell lines exists for some, but not all chemicals, and found no evidence for the heritability of toxicity response phenotypes for the chemicals we tested. We then investigated genetic factors contributing to wide variability in response by conducting genome-wide association scans. We conclude that the approach of screening chemicals for toxicity in a genetically-defined, yet variable in vitro human cell-based system is potentially useful for identification of both chemicals and individuals that may be at highest risk, as well as the within-species degree of variability in the population, and genetic loci of interest that potentially contribute this phenomenon.