Introduction The co-occurrence of ring chromosome 13 syndrome and 47, XYY syndrome in the same individual is rare. To the best of our knowledge, this is the first report of the co-existence of this kind of chromosome aberrations. At present, the deletion 13q syndrome is divided into three groups based on the deletion's location relative to chromosomal band 13q32. Group 1 (proximal to q32) and group 2 (including q32) have shown distinctive phenotypes including mental retardation and growth deficiency. Group 3 (q33-34 deletion) is defined by the presence of mental retardation but there is usually an absence of major malformations. Case presentation We describe a 10-month-old Chinese Han boy presenting with severe mental retardation, profound congenital bilateral hearing loss with a terminal 13q33.2 deletion and multiple malformations. Routine chromosome analysis disclosed a de novo complex karyotype 47, XYY, r(13)(p11q34). Further investigation by high resolution array-based comparative genomic hybridization delineated an 8.5 Mb terminal deletion on the long arm of chromosome 13(13q33.2→q34). Conclusion The co-occurrence of double syndromes in the same individual is rare and its clinical presentation is variable depending on the predominating abnormality or a combination of the effect of both. Hearing impairment is suggested as another new clinical feature to 13qter deletion. This case report will contribute to more accurate genetic counselling and provide further insight to the syndrome.