Two of three unrelated children with de novo congenital complex chromosome rearrangements (CCR) with more than four chromosome breaks had cleft lip and palate as one of several congenital anomalies. In patient 1, unilateral complete cleft of the primary and secondary palates accompanied severe ectrodactyly, bilateral posterior choanal atresia and several minor congenital anomalies. Karyotypes of peripheral lymphocytes and skin fibroblasts showed five derivative chromosomes with six break points. There were two translocations, t(2;5), t(3;11) and an interstitial deletion, del(13)(q12q14). Patient 2 had a bilateral complete cleft of the lip and palate, in addition to slow pre- and postnatal growth and minor congenital anomalies. Peripheral lymphocytes and palatal mucosa fibroblasts karyotypes showed five derivative chromosomes with six break points. A partial deletion of 10p, two translocations, t(2;3), t(7;18) and an inversion of the derivative chromosome 2 were present. In both patients, a "major catastrophe" of unknown etiology in one of the parental gametes appeared to be the event leading to the stable CCR without evidence of persistent chromosome instability. All four parents had normal karyotypes. The presence of palatal clefts in these patients indicates that dysmorphologists and pediatricians have to consider CCR whenever taking care of a patient with cleft palate, particularly if additional anomalies, no matter how subtle, are present. The detection and interpretation of the latter anomalies are essential for the diagnosis and management of these patients. Accurate cytogenetic diagnosis determines the short- and long-term prognosis and facilitates genetic counseling in regard to life-span, quality of life and reproductive plans of patients and parents.