We describe a 14-year-old boy with congenital bilateral cataracts, blepharophimosis, ptosis, choanal atresia, sensorineural hearing loss, short, webbed neck, poor esophageal motility, severe growth and mental retardation, skeletal anomalies, seizures, and no speech. As an infant, he had transient hypogammaglobulinemia requiring IVIG therapy. Cytogenetic studies show an apparently de novo visible duplication at 1p36.3. Fluorescence in situ hybridization (FISH) studies confirm that the common region for the 1p36 deletion syndrome (p58) is duplicated. Probes for D1Z2 at 1p36.3 and the subtelomeric region of 1p (TEL1p) are also duplicated. Array comparative genomic hybridization (aCGH) studies were done at three separate laboratories, each with somewhat different results. BAC whole genome array CGH suggests a single clone gain at the 1p terminus and a single clone deletion at 1p36.3. A targeted BAC array panel with higher resolution at the distal 1p36 region detects a telomeric duplication and an interstitial deletion. Oligonucleotide whole genomic aCGH shows the highest resolution and a more complex rearrangement: two duplications, an interstitial deletion, and a normal region. The MMP23A/B “matrix metalloproteinase 23A/B” genes are within the distal duplication region in our patient, and this patient does not have craniosynostosis. This is the first association of congenital cataracts, choanal atresia, and transient immune abnormalities with 1p36 duplication/deletion. This case illustrates the limitations of different cytogenetic technologies, and shows how three separate aCGH platforms allow for refined delineation and interpretation of the complex cytogenetic rearrangement which would not have been discovered by standard high-resolution chromosome analysis. © 2008 Wiley-Liss, Inc.