The early palindrome domain within the SV40 core origin of replication is essential for the initiation of replication. Studies with single point mutants in this region suggested that the early palindrome domain does not function as a cruciform structure(1), but may be involved in the initiation of SV40 DNA replication in a sequence-specific manner. Two mutants, base-substituted at a primase initiation site nucleotide 5214(2), showed dramatic decreases in DNA replication in monkey cells. Despite earlier reports to the contrary (3,4), disruption of the cruciform configuration or polypyrimidine tract does not invariably lead to lack of replication function, as some mutants unable to form this structure replicate normally. Gel retention assays and DNase I footprinting with the nuclear proteins of monkey cells showed that the 5′GAGGC3′ pentanucleotide repeats on either side of early palindrome domain interact with monkey nuclear protein. The early palindrome domain may affect the interaction of SV40 DNA with nuclear protein, and participate in SV40 DNA replication.