Abnormalities in DNA metabolism have been found in third-instar females of Drosophila melanogaster that are heteroallelic or homoallelic for X-chromosomal giant (gt) mutations. Analysis of DNA metabolism in larval brain ganglia was carried out using alkaline sucrose gradient centrifugation, incorporation assays and a neutral filter elution assay. These analyses show that gt stocks synthesize DNA of a reduced molecular weight, have an unusually high frequency of spontaneous single and double-strand breaks, and exhibit a reduction in the normal inhibition of DNA synthesis following treatment with UV and the carcinogen AAAF. These phenomena are not associated with a defect in the repair of X-ray induced DNA breaks nor are they accompanied by any alterations in chromosome stability. Analysis of homozygous 1(2)gl larvae also reveal that these phenomena are specific to the gt locus and are thus not attributable solely to an extended developmental program. These findings strengthen the suggestion that the genetic instability associated with gt is related to perturbations in chromosome metabolism (Green 1982).