Here we report the cloning and characterization of a novel PDE4D isoform (PDE4D11) identified in mouse brain cDNA. This novel isoform has a unique isoform-specific 5'-UTR and N-terminal sequence, whereas, downstream regulatory N-terminal and catalytic C-terminal regions are homologous to other long PDE4D isoforms (Ex2-15). In silico analysis of PDE4D11 cDNA transcript identified the predicted translational start site and the use of a different transcriptional start site compared to other PDE4D isoforms. This isoform is ubiquitously expressed in different mouse tissues, particularly in the brain, liver and spleen. In the brain, PDE4D11 expression levels increased in the cerebellum, but decreased in the hippocampus with progressive age, highlighting a potential role for this isoform in the development of the brain. When transfected in vitro into murine neuroblastoma cells PDE4D11_EGFP expression is cytosolic, consistent with other long PDE4D isoforms. The appearance of cytosolic protein aggregates in discrete microdomains with this isoform, however, may represent a method of compartmentalizing PDE4D11 activity. The novel 5'-sequence of PDE4D11 is conserved among higher vertebrates including human, monkey, dog, horse and rat. Identification of this new isoform highlights the mutliplicity of unique PDE4D isoforms and their potential importance in regulating cAMP levels through compartmentalization and cell-specific expression and underscores the importance of understanding the functional role of each isoform in the development of specific drugs for the treatment of memory disorders.