The heart is a unique organ that is able to use several fuels for energy production. During development the heart undergoes changes in supply of fuels and must be able to respond to these changes. We have examined changes in expression of several genes that regulate fuel transport and metabolism in the rat heart during early development. At birth, there was increased expression of fatty acid transporters and enzymes of fatty acid metabolism that allow fatty acids to become the major source of energy for cardiac muscle during the first two weeks of life. At the same time, expression of genes that control glucose transport and oxidation was down-regulated. After two weeks, expression of genes for glucose uptake and oxidation was increased, and expression of genes for fatty acid uptake and utilization was decreased. Expression of carnitine palmitoyltransferase-I (CPT-I) isoforms during development was different from published data from rabbit hearts. CPT-I and CPT-I isoforms were both highly expressed in the heart before birth, and both increased further at birth. Only after the second week did CPT-I expression fall appreciably below the level of expression of CPT-I. These results represent another example of different expression patterns of CPT-I isoforms among different mammalian species. Changes found in gene expression in rats followed nutrient availability during development and may render cardiac fatty acid oxidation less sensitive to factors that influence malonyl-CoA content (e.g. fluctuations in glucose concentration), and thereby favor fatty acid oxidation as an energy source for cardiomyocytes in early development.