CD44 is a cell-surface molecule that has been shown to have several splicing isoforms. In various human tumors, such as primary colon and breast tumors, and their metastases, alterations of CD44 isoform expression have been reported. The present study was performed to investigate CD44 alternative transcript splicing in gynecologic malignancies. We performed reverse transcriptase polymerase chain reaction (RT-PCR) analysis of CD44 splice variant expression on mRNA transcripts from ovarian carcinomas (six primary and 15 metastatic tumors) from 21 patients and from cervical carcinomas (25 primary and two metastatic tumors) from 25 patients. We also performed this analysis on five different ovarian carcinoma cell lines established from ascitic fluid and primary tumors, and two cervical carcinoma cell lines. We included eight normal female genital tissue specimens and one additional placenta specimen in our RT-PCR analysis for comparison with CD44 expression of carcinomas. The CD44H isoform was amplified in all of the specimens. None of eight normal tissue specimens, including myometrium and ovary, expressed CD44R1 transcripts. But the CD44R1 transcript was expressed in 2/6 (33.3%) primary ovarian carcinomas and in 7/15 (46.6%) metastatic ovarian carcinomas. In cervical carcinoma, 13/25 (52.0%) primary tumors and 2/2 (100.0%) metastatic tumors expressed CD44R1. The CD44R1 transcript was expressed increasingly during ovarian and cervical tumor progression (P = 0.026 and P = 0.002, respectively). In conclusion, the frequency of CD44R1 transcript expression increased during ovarian and cervical carcinoma progression, and analysis of CD44 splice variants may be useful in detecting primary and metastatic gynecologic malignancies.