AAV is a known contaminant of adenovirus preparations including stocks of human, simian, bovine, avian, and canine adenoviruses. While other viruses, such as HSV and vaccinia, can function as helper viruses for AAV replication in vitro, AAV has not been identified as a contaminant of these viral preparations. In order to to identify helper viruses that allow propagation of AAV and to identify and characterize novel AAV isolates, we screened about 100 viral stocks, supplied by the American Type Culture Collection (ATCC) for the presence of AAV DNA using a PCR based assay. These samples included adenovirdae, herpesviridae, retroviridae, coronaviridae and orthomyxoviridae. Thirty-three percent of the adenovirus stocks screened were contaminated with AAV with the highest percentage (79%) found in human and non-human primate adenovirus samples. We were unable to detect AAV in any other virus family tested, suggesting that adenoviruses are the preferred helper virus. We cloned and sequenced the genomes of AAVs found in ten simian adenovirus isolates. These novel AAV isolates displayed at least 98% homology in the capsid ORF to either AAV1, AAV6, or to each other. The majority of divergent amino acids between the novel AAVs and AAV6 are located on the surface of the virus surrounding the 3-fold axis of symmetry, in an area of the capsid that has been associated with receptor binding. Despite their high homology to AAV-6, we observed a distinct cell tropism of the novel AAV isolates and differences in sensitivity to lectin competition, suggesting that these novel isolates may utilize a distinct entry pathway. These novel AAVs might prove useful for gene therapy applications and we are currently investigating the use of the novel AAV isolates in in-vivo gene transfer.