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Background Chimaerism is a rare genetic condition where an individual possesses two or more distinct cell lines originating from different zygotes. This case report highlights the diagnostic challenge presented by pseudochimaerism in a patient initially diagnosed on oligonucleotide microarray with mosaic Klinefelter syndrome (47,XXY).Methods A 3-year-old boy, a dichorionic diamniotic twin, delivered at 35 weeks of gestation with developmental delay, spastic diplegia and tiptoe walking, had chromosome testing carried out using a 60K oligonucleotide microarray. The microarray identified a gain of a whole X chromosome at a low level, consistent with a diagnosis of mosaic Klinefelter syndrome. The parents were informed of this diagnosis, and the family was referred to the clinical genetics service.Results The family was seen in the clinical genetics service, and the likely diagnosis was explained. Subsequent confirmatory blood karyotype analysis revealed two distinct cell populations, 46,XX and 46,XY, indicating pseudochimaerism as an explanation for his array finding, rather than mosaicism for Klinefelter syndrome.Conclusion This case demonstrates the diagnostic challenges and the need for confirmatory genetic testing in patients diagnosed with Klinefelter syndrome on oligonucleotide microarray.