Notch1 protein is a transmembrane receptor that directs various cell fate decisions. Active forms of Notch1 consisting of a transmembrane domain and an intracellular domain (Notch1TM) or only an intracellular domain (Notch1IC) function as oncoproteins. To elucidate the effect of Notch1 abnormalities in radiation-induced lymphomagenesis, we determined the structure of the Notch1 gene and examined the frequency and the sites of Notch1 rearrangements in radiation-induced mouse thymic lymphomas. The Notch1 gene consists of 37 exons, including three exons upstream of the previously reported exon 1. The transcript starting from exon 1 was the major transcript whereas the transcripts read upstream from exon 1a, in which amino acid sequences in the N-terminal region were changed, were minor. More than 50% of radiation-induced thymic lymphomas exhibited Notch1 rearrangements, suggesting that Notch1 acts as a major oncogene in radiation-induced lymphomagenesis. We identified three rearranged sites: novel sites in the 5' end region encompassing exons 1 and 2, the previously identified juxtamembrane extracellular region, and the 3' end region. The 5' deletion and the insertion of murine leukemia virus in the juxtamembrane region led to the production of abnormal transcripts starting from cryptic transcription start sites located halfway through the Notch1 gene and resulted in transcripts lacking most of the extracellular domain. As a result of these rearrangements, truncated Notch1 polypeptides resembling Notch1TM or Notch1IC were formed. In contrast, the 3' deletion led to the production of a C-terminal PEST motif-deleted transcript. The downstream target gene Hes1 was transcribed in a lymphoma with insertion of murine leukemia virus, but not in a lymphoma with a 5' deletion. These results indicate that in addition to Hes1 expression, other Notch1 pathway(s) have a role in thymic lymphomagenesis and suggest the presence of a novel mechanism for oncogenic activation of Notch1 by 5' deletion.