Background: A cytogenetical study should be performed to every newborn with malformations. If a chromosomal aberration is found, parents must be studied to give an adequate genetic advise. Aim: To study the frequency of chromosomal aberrations in newborns with malformations. Patients and methods: In the Clinical Hospital of the University of Chile all malformations in newborns are registered, as part of the Collaborative Latin American Study of Congenital Malformations (ECLAMC). The frequency of chromosomal aberrations, determined by cytogenetical studies, was determined in newborns with malformations. Results: In the study period, there were 32,214 births. Of these, 2,268 live newborns and 43 stillbirths had malformations. Ninety nine children with malformations had chromosomal aberrations (4.3%). Trisomy 21 was the most common aberration with a rate of 23/10,000 births, followed by trisomy 18 with a rate of 4/10,000 and trisomy 18 with a rate of 1.2/10,000. Ninety four percent of these children were born alive and 16.1% died before discharge from the hospital. The masculinity indexes for Down syndrome and for trisomy 18 were 0.38 and 0.61 respectively. Conclusions: A higher frequency of female gender for trisomy 21 and male gender for trisomy 18 has not been reported previously (Rev Méd Chile 2003; 131: 651-658)