PAX6 encodes a transcriptional regulator that is essential for brain morphogenesis. Heterozygous PAX6 mutation is associated with aniridia and abnormalities of the interhemispheric pathway in humans. We present the case of a 12 year old boy with a known mutation of the PAX6 gene. There were parental concerns regarding his hearing, but repeated pure-tone audiograms were normal. He had a battery of standard central auditory tests, which gave abnormal results in tests which required auditory interhemispheric transfer (dichotic digits and pattern tests). A speech and language assessment, which yielded age-appropriate scores for speech, receptive and expressive language, revealed impaired verbal working memory. These test results were interpreted as indicating impaired auditory sensory and higher order interhemispheric transfer, consistent with reported findings in adults with mutations in PAX6, and correlated with his parent-reported hearing difficulties. This is the first report of central auditory and verbal working memory deficits in a child with a PAX6 mutation. Further research is needed to assess how these deficits impact on academic performance particularly in childhood.