Rapidly growing wild-type Escherichia coli cells contain two, four, or eight fully replicated chromosomes after treatment with rifampin, reflecting that all replication origins are initiated simultaneously. Cells with defects in the timing of the initiation of replication may contain three, five, six, or seven fully replicated chromosomes after such treatment. This phenotype, termed the asynchrony phenotype, is also seen in recombination-deficient recA mutants. It is shown here that for recA strains, the phenotype can be explained by a selective and complete degradation of individual chromosomes. The selective degradation is largely recD dependent and is thus carried out by the RecBCD exonuclease.