We generated DNA probes for CD44 variable region exons 11 (v6) to 14 (v9) and also for intronic sequences and examined the expression of aberrant CD44 transcripts in digestive tract carcinomas, colorectal adenomas and intestinal metaplasia of the stomach. The study used the reverse transcription-polymerase chain reaction/Southern blot technique. Among the probes generated, the CD44 intron 9 probe was the best for distinguishing cancer tissue from normal tissue in adenocarcinomas of the colorectum or stomach. All the colorectal adenocarcinomas revealed overexpression of CD44 variants containing the intron 9 sequence compared with the corresponding normal colorectal mucosa. The overexpression of such abnormal CD44 variants was observed from an early stage in colorectal cancer and did not correlate with nodal or distant metastatic status. In intestinal metaplasia of the stomach, aberrant CD44 transcripts with characteristic 2 or 3 peaks containing intron 9 were observed. On the other hand, in oral and esophageal squamous cell carcinomas and corresponding normal squamous epithelia, overexpression of CD44 variants with variable exons and retained intron 9 sequence was frequently observed in both cancer tissue and corresponding normal mucosa. Examination of the expression of CD44 variants in a screening panel of normal tissues from the whole body revealed that overexpression of transcripts containing exon 11 and 14 as well as of the intron 9 sequence was constantly observed in tissues with squamous epithelia like skin, oral mucosa, esophagus and uterine cervix. Expression of these variants was also found in urinary bladder, respiratory tract, pancreas and salivary glands. Our results overall indicate that detecting the overexpression of abnormal CD44 transcripts, especially ones containing the intron 9 sequence, could be a powerful indicator for the presence of adenocarcinomas in the digestive tract. However, it is not applicable for the diagnosis of malignancies originating from squamous epithelia.