We describe a de novo apparently balanced reciprocal translocation, 46,X,t(X;16)(q28;q11.2), in a 13 year old girl with median cleft of the upper lip, pedunculated skin masses on the nasal septum, short stature, and mental retardation. Pai syndrome is characterised by median cleft of the upper lip, pedunculated skin mass(es) on the face, and midline lipoma(s) of the central nervous system. The cause of this syndrome is unknown, although autosomal dominant inheritance has been proposed. The translocation breakpoints in the present patient may be candidate regions for a gene responsible for median cleft of the upper lip and pedunculated skin mass(es) on the face, including Pai syndrome.