Endomyocardial biopsies are the criterion standard in diagnosing acute cardiac transplant rejection. This study sought to analyze mRNA expression profiles of various immuneresponse-related genes in endomyocardial biopsies of heart transplant patients and to correlate the results with histologic findings.Forty-three biopsies obtained from 6 heart transplant recipients experiencing acute rejection were analyzed for granzyme B, CTLA4, IL-6, TGF-beta, and TNFa expression using real-time polymerase chain reaction. The results were compared with the histologic findings. Biopsies obtained before, during, and after acute rejection episodes were grouped according to the International Society of Heart and Lung Transplantation standard biopsy grading from 1990. Group 1 consisted of biopsies with International Society of Heart and Lung Transplantation grade 0 (n=12), group 2 of International Society of Heart and Lung Transplantation grade 1A (n=14), and group 3 of International Society of Heart and Lung Transplantation grades 1B, 2, 3A, and 4 (n=17).A strong correlation was seen between histologic groups and gene expression of granzyme B, which showed the highest overall transcript levels. CTLA4 was elevated in group 2, but no further increase in the rejecting group 3 was seen. For IL-6, TGF-beta, and TNFa gene expression was strongly elevated in group 3 compared with groups 1 and 2. On analysis of biopsies with International Society of Heart and Lung Transplantation, grade 0 and 1A, relative to the time point of rejection, we found a substantial increase in mRNA expression of all analyzed immune response-related genes before a rejection episode. The strongest up-regulation was seen for granzyme B, TNFa, and TGF-beta.Our data suggest that analyses of gene expression provides valuable information in diagnosing heart transplant rejection. Furthermore, analyses of granzyme B, TGF-beta, and TNFa might not only confirm an ongoing rejection episode, but also may have a positive predictive value.