V(D)J recombinase activity was measured in an array of human cell lines derived from hematopoietic malignancies representing various lineages and developmental stages. The level of recombinase activity was found to vary over a 2000-fold range between different cell lines. Several myeloid cell lines were positive for V(D)J recombinase activity, providing additional insight into the relationship between myeloid and lymphoid differentiation. Despite high levels of V(D)J recombination in two human acute lymphoblastic leukemia cell lines, the cytogenetic karyotype has remained essentially constant over several years of continuous cell culture. Silencing of recombination of chromosomal and minichromosomal targets has been strongly correlated with the replication of CpG methylated DNA in murine cells. Here, in human cells, we show that human minichromosomes bearing V(D)J recombination signals are protected well over 100-fold from recombination if they are CpG methylated, providing a rational basis for the karyotypic stability in cells with high levels of V(D)J recombination activity.