We report on a 2-year-old boy with intellectual disabilities, distinctive facies, hypotonia, cardiac, and renal malformations. During his infancy he had recurrent episodes of apnea, cyanosis, and bradycardia. Chromosomal analysis showed a de novo apparently balanced translocation 46,XY,t(9;15)(q31;q26)dn. The use of array-comparative genomic hybridization (CGH) however, revealed the presence of additional cryptic complex chromosomal rearrangements involving a approximately 5-5.8 Mb distal duplication on chromosome 9 (9q34.1 --> 9q34.3), and deletions on three separate regions of chromosome 15 adding to approximately 8.1-12.2 Mb (15q21.2 --> 15q21.3, 15q22.31 --> 15q23, 15q25.1 --> 15q25.2). During confirmation with fluorescence in situ hybridization (FISH) an inversion was unexpectedly revealed on chromosome 15 (15q21.1 --> 15q21.2). To our knowledge this is the first patient reported whose phenotype is due to partial trisomy 9q, and complex interstitial deletions of 15q, not involving the Prader-Willi/Angelman region and encompassing the critical region 15q21q25. We provide correlation between the clinical findings of our patient and the phenotype of the 9q34 duplication syndrome, the 15q21, and the 15q25 deletion syndromes.