Germline TCR-V beta transcription is commonly considered an event coupled with rearrangement of TCR genes in T cells. The extent of germline V beta transcription is studied here in a range of cell types and in several mouse strains. A sensitive semi-quantitative RT-PCR method was developed to specifically detect germline and not rearranged transcripts. Germline transcription of a range of different V beta genes was detected along with rearranged transcripts in bone marrow, thymus, mesenteric lymph node and spleen. Some transcripts were also detected in low level in non-lymphoid tissues including heart, liver and brain. Expression was also studied in the C57BL/6J-beta(2)microglobulin(-/-) (C57BL/6J-beta M-2(-/-)) mouse model that lacks NK1.1 T cells and predominantly utilises V beta 8.2 in the formation of a TCR. beta M-2(-/-) mice, which lack both CD-dependent NK1.1 T cells and CD8(+) T cells, showed germline TCR-V beta 8 transcription in most tissues indicating that germline transcription is not specifically related to CD1-dependent NK1.1 T cells. In many tissues, multiple transcripts were amplified representing both spliced and unspliced forms of germline V beta. For most V beta genes, the expression of spliced and unspliced forms was equivalent. Given an abundance of unspliced transcripts, the presence of alternative ORFs encoding a novel protein was investigated within the TCR-V beta genes. Sequence analysis of ORFs showed only genes with a high level of similarity to TCR-beta. All data reflect the prevalence of germline transcripts in vivo and raise questions about their functional role. (c) 2007 Elsevier Ltd. All rights reserved.