CD69 is the earliest inducible cell surface glycoprotein acquired during lymphoid activation. CD69 functions as a signal transmitting receptor involved in cellular activation events including proliferation and the induction of specific genes. This molecule is a member of a supergene family of type-II integral membrane proteins with C-type lectin domains. We have herein studied the genomic structure of the human gene encoding CD69. The coding sequence is divided into five exons separated by four introns. The first two exons corresponded to separate functional domains of the protein (cytoplasmic tail and the transmembrane region), while the final three exons encoded the carbohydrate-recognition domain (CRD). The conserved intron position between the exons encoding the CRD indicated that this protein is closely related to other type-II receptor groups with the C-type CRD, such as the asialoglycoprotein receptors, the low-affinity IgE receptor (CD23), and natural killer cell-specific receptors, NKR-P1 and Ly49. In contrast to the broad NKR-P1 and Ly-49 gene families, CD69 is a single-copy gene, as demonstrated by Southern blot analyses. The major transcription initiation site has been located, by amplification of cDNA 5′ ends, 30 nucleotides downstream of a consensus TATA box. Comparison of human CD69 and mouse NKR-P1 gene structures indicates that the first intron maintains a conserved position, suggesting that CD69 and this gene family may diverge from a common ancestor gene. A possible evolutionary pathway of these genes is proposed.