Increased nuchal translucency between 10 and 14 weeks of gestation has now been established as a marker for chromosomal defects in several large-scale studies. In addition, a growing number of structural defects and some rare genetic syndromes have been identified in association with this marker. We describe a case of a fetus with increased nuchal translucency at 12 weeks of gestation, in which second-trimester evaluation by ultrasound showed an enlarged cisterna magna, a ventricular septal defect and moderate signs of dysmorphia. Karyotyping by chorionic villus sampling revealed a high rate of chromosomal breaks. The diagnosis of Fanconi anemia with early onset was confirmed following the development of severe postnatal anemia 2 months after birth.