The CD44 cell surface hyaluronan binding protein has many isoforms formed by alternative splicing and glycosylation, and some variants have been associated with a malignant phenotype, invasion and metastasis. CD44 splicing patterns and intron 9 retention in 24 oro-pharyngeal squamous cell carcinomas (OSCC) were investigated by RT-PCR. Transcription efficiency and quantity were determined in 10 carcinomas and normal control mucosa by real-time PCR using dual-labeled fluorescent Taqman probes. Most of the carcinomas, regardless of grade, showed one major transcript including exons v2-v10, similar to that expressed by normal keratinocytes. In addition, most carcinomas expressed a variety of truncated transcripts of contiguous variant exons. Real-time PCR revealed that carcinomas showed both over-expression and down-regulation in transcription compared to normal keratinocytes, but this change was independent of the state of differentiation or the sub-site of biopsy. Intron 9 was not retained in normal keratinocytes or carcinomas. Overall, the results indicate that OSCC, like normal keratinocytes, constitutively express all variant exons and that the missplicing seen in other malignancies does not appear to occur. OSCC do not reproducibly over-express CD44 and show a wide range of transcription levels. CD44 expression does not appear to be fundamentally deranged in OSCC and is unlikely to be of value in early diagnosis, or as a prognostic marker.