We report on a patient with a mild clinical phenotype, including genital anomalies, with mosaic tetrasomy 9p. Karyotype analysis of peripheral blood lymphocytes detected a supernumerary isochromosome 9p present in every cell, with the initial result being reported as tetrasomy 9p in non-mosaic form. However, array Comparative Genomic Hybridization (aCGH) studies on DNA extracted from peripheral blood lymphocytes and saliva showed that the patient had tissue-specific mosaicism, with a lower level of abnormal cells in the saliva. These results correlate with the patient's clinical features as non-mosaic cases of tetrasomy 9p have a more severe, often lethal, clinical phenotype. If non-mosaic tetrasomy 9p is identified in a peripheral blood culture then examination of a different tissue type should be undertaken. Array CGH may be used as an alternative to karyotype analysis to estimate the level of mosaicism, and may eliminate the need for invasive skin biopsy as samples such as buccal smear and saliva can be used. Array CGH is able to detect mosaicism, establish the euchromatic content of supernumerary marker chromosomes, and identify imbalances elsewhere in the genome allowing more accurate counselling and prognosis for patients. © 2011 Wiley-Liss, Inc.