Objectives: To describe the molecular analysis through comparative genomic hybridization (CGH) of fetuses with gastroschisis, and to observe if this technique could improve the resolution of the conventional cytogenetic techniques. Methods: Amniotic analysis of fetuses with gastroschisis, using both conventional (G-banding) and molecular (CGH) cytogenetics assays. Results: All of the seven fetuses studied displayed a normal G-band karyotype. Six fetuses displayed a normal disomic profile through CGH and one sample has displayed ish cgh enh 3q26 -> qter result (ICSN). The fetus with this imbalance of chromosome 3 was re-classified as a ruptured omphalocele, instead of gastroschisis, after birth. Conclusions: The molecular investigation through CGH technique can improve the resolution of the conventional karyotye analysis in cases of abdominal wall defects. Copyright (c) 2007 S. Karger AG, Basel.225361364