We have isolated and characterized the gene coding for the alpha subunit of the rat mast cell high affinity IgE receptor. The gene comprises five exons and four introns and spans approximately 6.6 kilobases. The leader sequence is encoded by two exons, the second of which is only 21 base pairs long. The third and fourth exons each code for repeating immunoglobulin-like extracellular domains. A hydrophobic transmembrane domain and positively charged cytoplasmic tail are encoded by a single final exon. The sequence of the 5'-flanking region was determined, and the major transcription initiation site was mapped. The structure of the gene suggests that two minor species of RNA produced by rat basophilic leukemia cells are due to alternative splicing. In one case, the small second exon is removed entirely, and, in the other, 163 base pairs at the 3' end of the fourth exon are removed. The latter species of RNA suggests the possibility of a secreted form of the alpha chain of the receptor. A third variant species of RNA, lacking a leader sequence, may be due to use of an alternative transcription initiation site.