5-Azacytidine (azaCR) causes genomic demethylation and decondensation of juxtacentromeric heterochromatin in chromosomes 1, 9, and 16. We determined the karyotypes of a pro-B cell line (FLEB14) treated with azaCR or its deoxynucleoside analog (azaCdR). About 80% of the induced rearrangements were in chromosome 1, and almost 90% of these involved its pericentromeric region. Multibranched figures with up to seven chromosome 1 arms, as well as whole-arm deletions of this chromosome, were the predominant anomalies, often with one normal homolog of chromosome 1 present. Isochromosomes 1 and fusions in the pericentromeric regions of chromosomes 1 and 16 or chromosomes 1 and 9 were also seen. The overlap of the spectrum of chromosomal rearrangements in azaCR- or azaCdR-treated FLEB14 cells and in mitogen-stimulated lymphocytes from patients with a rare genetic disease (ICF) associated with localized DNA hypomethylation supports the hypothesis that the DNA demethylating activity of azaCR is essential for the induction of these pericentromeric rearrangements. These studies may help elucidate the overrepresentation of chromosome 1 pericentromeric rearrangements in many types of cancer cells.