Polycystic kidney disease is characterized by abnormal morphological development. Mechanisms that regulate cyst development may involve multiple signaling pathways. Cyst formation by Madin-Darby canine kidney (MDCK) cells in three-dimensional culture is assumed to be cyclic AMP-dependent and due to cyclic AMP-dependent protein kinase (cAPK) activation based on pharmacological responsiveness. To determine if different cyclic AMP (cAMP) pathways are associated with morphological development, the role of cAMP in regulating morphological change was examined in MDCK clones that form tumor-like or tubular structures under basal conditions. Pharmacological cAMP pathway activators induce cyst formation and diminish formation of other structures in three clones, whereas one clone is unaffected. Tyrosine kinase-mediated morphogens have little effect. Although all clones have intact cAMP signaling pathways, each has a unique subcellular distribution of cAPK regulatory subunits. This may reflect distinct mechanisms for cAPK anchoring, allowing cAPK subtype regulation of the unique phenotypic character of each clone through preferential access to substrates. These observations suggest a molecular basis for differential cAMP responsiveness in cells that develop distinct morphological phenotypes. This evidence establishes these MDCK clones as models for understanding the mechanism and functional significance of cAPK subunit localization and may have broader implications for cystogenesis in polycystic kidney disease.