We report on a new chromosomal finding in a newborn male with hypertelorism, apparently low-set malformed ears with patent canal, micrognathia with narrow high-arched palate, bilateral webbing of neck with low posterior hairline, widely spaced nipples, and complex heart anomalies. Initially, what appeared to be a simple paracentric inversion of the long arm of chromosome 9, that is, 46,XY, inv(9)(q31q34) by routine GTG-banding technique was later determined to be a paracentric inversion with deletion of the band 9q34.1 by FISH technique using an abl unique sequence DNA probe. Thus the cytogenetic diagnosis was modified to 46,XY,der(9) inv(9)(q31q34.1)del(q34.1). Nevertheless, the presence of telomeric repeat sequences in the inverted chromosome 9 suggests that either healing has occurred by adding [TTAGGG]n sequences to the non-telomeric end (q31) by the enzyme telomerase or telomeric sequences were not affected during this inversion process. This abnormality is a rare occurrence and has never been reported before either because of a high rate of lethality or it has been undetected by routine cytogenetic techniques. The other abnormal cases with apparent paracentric inversions could also have a complex nature with congenital anomalies associated with loss of "few" DNA sequences as exemplified here.