Monoterpene-induced/repressed genes were identified in regressing rat mammary carcinomas treated with dietary limonene using a newly developed method termed subtractive display. The subtractive display screen identified 42 monoterpene-induced genes comprising 9 known genes and 33 unidentified genes, as well as 58 monoterpene-repressed genes comprising 1 known gene and 57 unidentified genes. Several of the identified differentially expressed genes are involved in the mitoinhibitory transforming growth factor beta signal tranduction pathway, as demonstrated by isolation of the mannose 6-phosphate/insulin-like growth factor II receptor and the transforming growth factor beta type II receptor. The monoterpene-induced/repressed genes indicate that apoptosis and differentiation act in concert to effect carcinoma regression. Apoptosis is suggested by the cloning of a marker of programmed cell death, lipocortin 1. Consistent with a differentiation/remodeling process occurring during tumor regression, subtractive display identified YWK-II and neuroligin 1. Thus far, of the cDNAs putatively identified as differentially expressed in this complex in situ carcinoma model, 5 were tested, and each one has been confirmed to be differentially expressed. Additionally, many of the identified known genes are expressed as rare transcripts and exhibit small but significant changes in abundance. Together, these points demonstrate the unique utility of this new gene expression screen to identify altered gene expression in a complex in vivo environment.