A holoprosencephaly, hypertelorism, and ectrodactyly syndrome (HHES) was described in three previous cases in whom chromosomes were apparently normal. We report on a 3-year-old boy with HHES and a de novo apparently balanced t(2;4)(q14.2;q35) confirmed by fluorescent in situ hybridization. He had severe growth and mental retardation, lobar holoprosencephaly, hypertelorism, microphthalmos, and iris, choroid, and retina colobomata. Less-severe facial involvement correlates with the semilobar type of holoprosencephaly; limb defects consisted of foot ectrodactyly and syndactyly. All previous HHES cases were sporadic and of unknown cause. A cryptic imbalance secondary to the translocation (2;4) in our patient may explain the phenotype.