Polyomavirus (Py) DNA replication may be regulated to a low-level replication state in specific target cells in mice as well as in certain undifferentiated murine cell lines, such as embryocarcinoma (EC) cells. To investigate possible mechanisms by which such control may occur, we have examined the effects of ElA on Py DNA replication. Adenovirus ElA proteins repress transcriptional activation of various enhancers, including those of Py, and can stimulate DNA replication in quiescent cells, but ElA effects on Py DNA replication were unknown. We found that constitutive ElA expression in NIH 3T3 cells depressed Py DNA replication very strongly. Two F9 EC cell-selected Py enhancer variants, PyF441 and PyFlOl, were also examined because undifferentiated EC cells are hypothesized to have an ElA-like activity responsible for the Py restriction, and these variants activate Py DNA replication in cis in undifferentiated F9 cells. Both variants were repressed by ElA, indicating that EIA activity in 3T3 cells is not equivalent to undifferentiated F9 cell ElA-like activity. We also examined transient inducible ElA expression in cells supplying Py large tumor antigen (T-Ag). Py DNA replication was again repressed, and the inhibition increased with ElA induction. Analysis of TAg mRNA levels indicated that ElA repression of Py DNA replication was not an indirect result of depression of TAg transcription. This suggests that E1A may repress Py DNA replication by a more direct mechanism, possibly by blocking enhancer activation of DNA replication in a manner uncoupled with enhancer transcriptional control.