We present the first report of a female fetus with concomitant isochromosome 18q [i(18q)] and cloacal dysgenesis sequence. Prenatal sonographic examination at 15 weeks' gestation showed intra-uterine growth retardation, a normal brain, a normal spine, congenital megacystis and oligohydramnios. The pregnancy was terminated. The abortus displayed dysmorphic features of a high forehead, hypertelorism, a prominent nose with a bulbous tip, median cleft lip and palate, micrognathia, low-set ears, a short neck, a joint contracture at the wrist, prominent heels and pseudo-hermaphroditism. Necropsy confirmed an imperforate anus, megacystis, a phallic structure and cloacal dysgenesis sequence. Postnatal chromosomal investigation proved a pure de novo i(18q). Molecular genetic analysis by polymorphic microsatellite markers confirmed the maternal origin of the aberrant chromosome. The coexistence of cloacal dysgenesis sequence and i(18q) in this case shows a correlation between the disturbance of the caudal developmental field and the chromosomal abnormality with monosomy 18p and trisomy 18q. Our presentation also demonstrates the importance of perinatal cytogenetic analysis in malformed fetuses in order to uncover underlying genetic disorders.