Early region 1 (E1)-deleted human adenovirus (AV) recombinants have been shown to be powerful tools of gene transfer in vivo and in vitro and are considered for application in human gene therapy. We could detect increasing titers of E1-containing adenovirus in two independent E1 + E3-deleted recombinant AV stocks during multiple passages in 293 cells, most likely due to a recombinant event with the host cell genome. We show the deleterious effects of this E1-containing, mostly replication-competent AV subpopulation in vivo and compare different screening methods of AV stocks for its detection. These considerations are important for the safety of human gene therapy trials.