The 10q23.3 gene PTEN (phosphatase and Tensin homologue deleted on chromosome 10) or MMAC1 (mutated in multiple advanced cancers 1) was recently reported to undergo frequent mutation, including mutations and deletions in multiple advanced cancers. This study showed that the aberrant transcripts of this gene are frequently found in cancers of the digestive tract, paired non-cancerous tissues and normal peripheral mononuclear cells. Sequence analysis of the aberrant transcripts revealed three types of deletions: (i) a deletion junction with a splicing-like donor or acceptor sequence; (ii) several-base homology near or between the donor acceptor site at the deletion junction; and (iii) deletion with insertion. From these results, it is suggested that aberrant transcripts of PTEN/MMAC1 found by nested reverse transcription-polymerase chain reaction are a common (or natural) phenomenon unrelated to oncogenesis. The mechanism producing these aberrant transcripts needs further investigation. Using single-strand conformation polymorphism and direct sequencing to analyse for small base changes of the genomic DNA of the PTEN/MMAC1 gene revealed no point mutations or small base changes.