We report a new-born girl with partial trisomy of 4q28-qter and partial monosomy of 9p24-9ter. Our patient has choanal atresia, hypertelorism, wide nasal bridge, high arched palate, discrete nipples, heart defects, myoclonic seizures and various dysmorphic findings. Standard chromosomal analysis with G-banding with Trypsin-Giemsa revealed 46,XX,der(9)t(4;9)(q28;p24) resulting from the mother's t(4,9) (q28;p24) karyotype. Deletions of the terminal part of 9p and partial trisomy of chromosome 4q are rare chromosomal alterations. To our knowledge, this is the first report of choanal atresia in a patient with a partial trisomy of 4q28-qter and partial monosomy 9p24-9ter combination, which were detected by integrated cytogenetic and genomic analysis. (C) 2015 Elsevier B.V. All rights reserved.