We describe a newborn female with a de novo duplication of chromosomes 2q31.2 and 2q37.3, and a de novo monosomy 9p24.3. The clinical findings of this patient include congenital heart defects, dysmorphic facial features, hypotonia, feeding difficulties and microcephaly. Ultrasonographic prenatal findings were negative for foetal malformations. Only a mild pyelectasis was reported. This is the first report of molecular cytogenetic characterization of a partial trisomy 2q31.2-37.3 with monosomy 9p24.3.