A helper-dependent adenovirus vector (HD AdV) that lacks all the coding sequences of viral proteins from the vector backbone was developed to overcome the problem of host cellular immune responses against E1-deleted AdV. One of the limitations of the current HD AdV system is its relatively inefficient propagation compared with that of E1-deleted AdV, which deters application of the HD AdV, especially in large animal models, We hypothesized that the low titers might be due in part to defects in replication and packaging of the vector DNA. We propagated two HD AdVs with similar marker gene cassettes and stuffer sequences, using two different helper viruses, and determined the replication and packaging efficiencies of viral DNA. Our analysis indicated a difference in replication and packaging efficiencies between the two vectors, which resulted in different propagation efficiencies, Furthermore, dl309, which is similar to the wild-type virus, demonstrated superior helper function over that of the loxP-containing helper virus, AdLC8cluc. These findings may have significant implications for the design of improved production systems of HD AdVs.