Recent advances have allowed for improved retrovirus-mediated gene transfer, and therapeutic benefits have been described in patients. These successes have shown the potential of hematopoietic stem cell (HSC) gene therapy, but treatment-related leukemia and benign expansion of gene-modified clones have shifted the attention toward safety. The delayed onset of adverse events in gene therapy clinical trials emphasizes the importance of long-term integration site studies in large animal models. We have addressed safety by characterizing the genomic location of 555 integration sites of the three most commonly used integrating retroviral vectors, that is, gammaretrovirus, lentivirus, and foamy virus, in long-term repopulating cells from dogs. Gammaretroviral integrants showed the most significant frequency of occurrence very close (<2.5 kb) to transcription start sites, but a substantial portion of all three retroviral integrants were within 50 kb. Importantly, gammaretroviral integrants were found more frequently in and near proto-oncogenes, suggesting this retroviral system may be the most prone to adverse gene activation. These data suggest that gammaretroviral vectors may have the highest intrinsic risk, but also emphasize that no vector system can be defined as “safe” based solely on integration profile.