The expression of genes encoding T cell receptor (TCR) alpha was used to follow the development of the thymus and to analyze the distribution of T cells in zebrafish. In the thymus, expression was first detected, by in situ hybridization, at four days post fertilization. In RNA extracted from whole fish, TCRalpha transcripts were also detected at four days and reached adult levels at three weeks. At six weeks, TCRalpha was expressed throughout the thymus, whereas rag1 expression was localized to the peripheral regions. Expression of TCRalpha outside the thymus was detected at nine days. In adult peripheral organs, the greatest expression was in the pronephros, mesonephros and intestine; expression in the spleen became greater as fish age. Three new, relatively highly expressed, TCR Valpha families were identified. (C) 2003 Elsevier Ltd. All rights reserved.