The PDZ proteins such as hDLG, hScrib and MAGIs function as the membrane-associated protein scaffolds and have been shown to interact with the high-risk HPV E6s. In the present study, we identified a Golgi-associated PDZ protein, CFTR-associated ligand (CAL) as a cellular target of HPV16 E6 by the proteomic approach. HPV16 E6 specifically interacted with the PDZ domain of CAL through the carboxy-terminal PDZ-binding motif, and the interaction caused proteasome-mediated degradation of CAL. HPV16 E6 interacts with CAL more strongly and degrades it better than HPV18 E6 owing to the more compatible PDZ-binding motif. CAL was highly ubiquitinated by the E6/E6AP complex or by E6AP alone albeit less efficiently. By siRNA-induced depletion of HPV16 E6 in Caski cells, CAL was down-regulated at the transcription level, but was stabilized at the protein level, suggesting that HPV16 E6 mediates the proteasomal degradation of CAL in HPV-positive cervical cancer cells. E6AP alone can bind, destabilize and ubiquitinate CAL independent of E6. In HPV-negative cells, the suppression of E6AP expression increased the protein level of CAL. Taken together, CAL is likely a natural target protein of E6AP and undergoes the E6/E6AP-induced degradation in an HPV-infected state. The E6/E6AP complex may tightly regulate the vesicular trafficking processes by interacting with CAL, and such a modification can contribute to the development of cervical cancer. In addition, the E6AP-mediated regulation of CAL is supposed to be important for understanding the etiology of Angelman syndrome.