It has been well documented that dietary copper (Cu) deficiency causes a hypertrophic cardiomyopathy in rodent models. However, a possible alteration in gene expression has not been fully examined. The present study was undertaken to determine the effect of Cu deficiency on protein profiles in rat heart tissue with the combination of the isotope-coded affinity tag (ICAT) method and Western blotting analysis. Male Sprague-Dawley rats were fed diets that were either Cu-adequate (6.0 microg Cu/g diet n=6) or Cu-deficient (0.3 microg Cu/g diet n=6) for 5 week. The ICAT analysis suggested that high-salt buffer (HSB) protein profiles from heart tissue of Cu-deficient rats were different from those of Cu-adequate rats; seven major protein species differed by more than a 100% increase or a 50% decrease. With three available antibodies, our Western blotting analysis confirmed that there was an 85% increase in fibulin-5 (also known DANCE/EVEC) and a 71% decrease in cytochrome C oxidase (CCO) VIb subunit, but no change in succinate dehydrogenase complex (also known complex II) IP subunit in Cu-deficient rat heart. Collectively, these data may be useful in deciphering the molecular basis for the impairments of function related to the hypertrophic-cardiomyopathy of Cu-deficient rats.