The deposition of intramuscular adipose fat is an important factor in the quality of beef, particularly in Korean cattle and Japanese cattle. A better understanding of the differential mechanisms regulating the deposition and release of fat between intramuscular and external adipose tissues, particularly subcutaneous adipose tissues, would prove vital in understanding the deposition of intramuscular fat. A SAGE (serial analysis of gene expression) method was used to identify functionally active genes in adipose tissues and to compare the global gene expression profile between the subcutaneous and the intramuscular adipose tissues in Korean cattle. We detected 11268 tags, representing 3761 transcripts in the SAGE library of the subcutaneous adipose tissues. We detected 10830 tags, representing 2918 transcripts in the intramuscular adipose tissues. Comparison of gene expression patterns between subcutaneous adipose tissues and intramuscular adipose tissues revealed that 82 genes were differentially expressed at >2-fold levels. Among them, expression levels of 50 genes were higher in subcutaneous adipose tissues compared with intramuscular tissues, whereas those of 32 genes were higher in intramuscular adipose tissues. The genes that displayed >2-fold higher expression in subcutaneous adipose tissues included secreted protein acidic and rich in cysteine, annexin II, thyroid hormone receptor interactor 1, ferritin heavy chain polypeptide 1, cofilin, diacylglycerol O-acyltransferase and thymosin beta 4. Those that showed >2-fold higher expression levels in intramuscular adipose tissues included troponin t3, heat shock 70 kDa protein 1 and NMT2 (N-myristoyltransferase 2). Expression patterns of NMT2 and troponin t3 genes were examined during differentiation of 3T3-LI preadipocytes. NMT2 gene was actively expressed at both the growing stage of preadipocytes and the initial stage of differentiation of 3T3-L1 adipocytes, but its expression was reduced at the active stage of adipocyte differentiation. Troponin t3 gene was not expressed at the growing stage of preadipocyte, but it was actively expressed during differentiation of adipocytes. This implies that troponin t3 may play a positive role in intramuscular fat deposition of beef. Our SAGE experiment provides a differential gene expression profile in subcutaneous and intramuscular adipose tissues of Korean cattle. This information will be useful in developing method(s) to produce high-marble beef.