The acetyl-CoA carboxylase-alpha gene has two promoters, PI and PII. A variety of mRNA products result from this gene, depending on promoter usage and splicing events. We have investigated thyroid hormone regulation of acetyl-CoA carboxylase-alpha gene expression, using the reverse-transcription polymerase chain reaction with PI- or PII-specific primers. RNA was extracted from a range of tissues taken from hypo-, eu-, or hyperthyroid rats. PII-generated products were found in all tissues examined at similar levels and were not affected by thyroid state. Products derived from PI were also widely found but with more variable levels of expression. PI mRNAs were reduced in hypo- and elevated in hyperthyroid livers. In brown adipose tissue, more PI products were found in hypothyroid animals. Thus, thyroid hormone regulates the activity of the acetyl-CoA carboxylase PI promoter to influence fatty acid synthesis in a tissue-specific manner.