A previous report described restriction endonuclease analysis of white pock variants of red cowpox virus and their characterization as deletion mutants lacking certain sequences including the repetition from one specific terminus of the wild-type genome. Further analysis has confirmed the terminal deletion but demonstrated that this is compensated at the site of deletion by the presence of an inverted duplication of a variable amount of sequence from the opposite terminus, with the effect of restoring a terminal repetition and the covalent, terminal crosslink. Nine of 11 white pock variants showed a similar deletion of about 21 Mdal mapping contiguously from the right-hand terminus and extending into a 2.4 Mdal restriction fragment. Two white variants showed larger deletions of about 24 and 27 Mdal respectively. These deletions were compensated by a copy of sequences from the opposite terminus which ranged in size from 3 to 27 Mdal. No terminal deletions smaller than 21 Mdal were observed in cowpox white variants or in clones retaining the red phenotype. In contrast with other orthopoxviruses, no deletions involving the left-hand terminus were found. Some independent white isolates had similar sizes of sequence copied from the opposite terminus, but some sibling clones from a single, pock-purified white isolate with the same size of deletion had different sizes of duplicated sequence. Other siblings isolated from an independent, three times pock-purified white clone, itself derived from a single parental red pock, differed from each other in the size of both the deletion and the duplicated sequence. These observations suggest preference for deletion in a particular region, conjunction of the genome termini during DNA replication and a requirement for the preservation of symmetrical termini in orthopoxvirus genome function.