The coxsackie adenovirus receptor (CAR) is a component of the tight junction complex and involved in cell adhesion. Loss of CAR expression can affect cell adhesion which in the context of carcinogenesis may influence both invasion and metastatic spread. Functional inactivation of CAR may also result from the interaction with its soluble isoforms. To relate alterations of CAR expression to tumor progression, we aimed to establish a highly specific real-time PCR protocol for quantification of all splice variants. In the process of cloning, we identified a novel splice variant termed CAR4/6 that lacked exon 5 but retained exon 6 encoding the transmembrane domain. Localization of CAR4/6 in the cell membrane was confirmed by ectopic expression in HT1080 cells. Expression analyses using cDNA arrays revealed that most normal tissues, including those of the female genital tract, express full-length CAR (CAR6/7) but not CAR4/6. Differential expression of both CAR splice variants was validated in microdissected epithelia (n = 66) derived from normal cervical ectodermal tissue, high-grade cervical intraepithelial neoplasia (CIN2/3) and invasive squamous cervical carcinoma. CAR4/6 was not expressed in normal cervical tissue but in 42% of CIN2/3 and in most cervical carcinomas (p < 0.001). In contrast, CAR6/7 was detected in all of the microdissected samples. As for CAR4/6 expression levels of CAR6/7 were significantly lower in normal tissue as compared with CIN2/3 and cancer (p < 0.01). Ectopic expression of CAR4/6 in different cell lines enhanced the proliferative and invasive properties indicating a possible role in cancer progression.