Mitochondrial DNA is almost entirely maternally inherited. Thousands of copies of mitochondrial DNA are present in every nucleated cell and in most normal individuals these are virtually identical (homoplasmy). Mitochondrial DNA diseases may be caused by mutations in either mitochondrial (Nature 1988;331:717-719) or nuclear genes (Nature 1989;339(6222):309-311; Br J Hosp Med 1996;55:712-716) and hence give rise to maternal or autosomal patterns of inheritance. Antenatal diagnosis of mitochondrial diseases based on chorionic villus sampling is available for Mendelian disorders and the syndromes caused by mutations at bp 8993 (associated with both Leigh's syndrome or neurogenic weakness ataxia and retinitis pigmentosa). However, prenatal diagnosis of many other maternally inherited mitochondrial DNA diseases is less reliable because it is not possible to predict the way in which heteroplasmic mitochondrial DNA mutations segregate within tissues with confidence. This review focuses on the substantial progress that has been made recently, and on the applicability of prenatal diagnosis to genetic counselling in this field.