Approximately 95% of all Friedreich's ataxia (FA) patients are homozygous for a large GAA triplet-repeat expansion in the first intron of the Friedreich's ataxia gene (FRDA). The remaining cases are expected to be compound heterozygous with a GAA expansion on one allele and a point mutation on the other. Generally, the clinical diagnostic profile in this group of patients is indistinguishable from that in classic FA patients with homozygous expansions. This study describes a mildly affected patient who presents with only one expanded allele by Southern blot analysis. Point mutation screening shows a single base change in FRDA exon 3 resulting in a nonconservative amino acid replacement in the N-terminal portion of the frataxin protein. Extended family studies show that two of the patient's sibs are carriers of the expanded allele and one is a carrier of the missense mutation. This case study demonstrates the benefits of implementing a combined Southern blot and point mutation diagnostic protocol for compound heterozygous patients. By identifying both mutations, this procedure confirms the diagnosis of FA in patients with an atypical disease course and allows for more complete family studies.