Conjugated linoleic acid (CLA) is an effective agent in preventing mammary cancer in rats treated with a carcinogen. The appearance of a tumor mass is the net result of cell proliferation minus cell death. Thus, apoptosis could be an important mechanism in controlling clonal expansion of the early premalignant lesions. The overall objective of this report was to determine whether CLA stimulated apoptosis. In the first part of the study, CLA was found to increase chromatin condensation (visualized through fluorescent 4',6-diamidino-2-phenylindole staining to DNA) and to induce DNA laddering, both evidence of apoptosis, in a rat mammary tumor cell line. The second part was to investigate the effect of CLA feeding on the development of histologically identifiable premalignant lesions in the rat mammary gland, as well as on the quantification of apoptosis (by terminal uridyltransferase nick end labeling assay) and the expression by immunohistochemistry of apoptosis regulatory proteins (bcl-2, bak, and bax) in normal versus premalignant mammary structures. CLA inhibited the formation of premalignant lesions by approximately 50%. It also significantly increased apoptosis and reduced the expression of bcl-2 in these lesions, but it did not modulate the levels of bak or bax. In contrast, neither apoptosis nor any of the apoptosis regulatory proteins was affected by CLA in normal mammary gland alveoli or terminal end buds. The data suggest that early pathological lesions may be particularly sensitive to CLA. In addition to providing a molecular basis for elucidating the mechanism of action of CLA in cancer prevention, the research on CLA-responsive biomarkers also has a practical side because these assays can be applied to biopsied human tissue samples in future CLA intervention trials.