Bis-(2-chloroethyl) sulfide (sulfur mustard; SM) is a potent alkylating agent. Three treatment compounds have been shown to limit SM damage in the mouse ear vesicant model: dimercaprol, octyl homovanillamide, and indomethacin. Microarrays were used to determine gene expression profiles of biopsies taken from mouse ears after exposure to SM in the presence or absence of treatment compounds. Mouse ears were topically exposed to SM alone or were pretreated for 15 min with a treatment compound and then exposed to SM. Ear tissue was harvested 24 h after exposure for ear weight determination, the endpoint used to evaluate treatment compound efficacy. RNA extracted from the tissues was used to generate microarray probes for gene expression profiling of therapeutic responses. Principal component analysis of the gene expression data revealed partitioning of the samples based on treatment compound and SM exposure. Patterns of gene responses to the treatment compounds were indicative of exposure condition and were phenotypically anchored to ear weight. Pretreatment with indomethacin, the least effective treatment compound, produced ear weights close to those treated with SM alone. Ear weights from animals pretreated with dimercaprol or octyl homovanillamide were more closely associated with exposure to vehicle alone. Correlation coefficients between gene expression level and ear weight revealed genes involved in mediating responses to both SM exposure and treatment compounds. These data provide a basis for elucidating the mechanisms of response to SM and drug treatment and also provide a basis for developing strategies to accelerate development of effective SM medical countermeasures.Bis-(2-chloroethyl) sulfide (sulfur mustard; SM) is a potent bifunctional alkylating agent capable of modifying and crosslinking cellular macromolecules such as DNA and protein by nucleophilic attack (Papirmeister et al., 1991). SM exposure can produce debilitating pulmonary, ocular, and cutaneous injuries. After cutaneous exposure to SM, there is a dosedependent latent phase of 8 to 24 h that precedes clinical expression of tissue damage. Erythema occurs initially and is followed by vesication because of separation at the epidermal-dermal junction. This results in large fluid-filled lesions that are long-lasting and slow to heal (Papirmeister et al., 1991;Petrali and Oglesby-Megee, 1997). The formation of blisters is accompanied by a potent inflammatory response, observed as increased production of inflammatory mediators and infiltration of the exposure area by activated immune cells (Rikimaru et al