Cytochrome c oxidase (CIV) deficiency is among the most common childhood mitochondrial disorders. The diagnosis of this deficiency is complex, and muscle biopsy is used as the gold standard of diagnosis. Our aim was to minimize the patient burden and to test the use of a dipstick immunocapture assay (DIA) to determine the amount of CIV in non-invasively obtained buccal epithelial cells. Buccal smears were obtained from five children with Leigh syndrome including three children exhibiting a previously confirmed CIV deficiency in muscle and fibroblasts and two children who were clinical suspects for CIV deficiency; the smear samples were analysed using CI and CIV human protein quantity dipstick assay kits. Samples from five children of similar age and five adults were used as controls. Analysis of the controls demonstrated that only samples of buccal cells that were frozen for a maximum of 4 h after collection provide accurate results. All three patients with confirmed CIV deficiency due to mutations in the SURF1 gene exhibited significantly lower amounts of CIV than the similarly aged controls; significantly lower amounts were also observed in two new patients, for whom later molecular analysis also confirmed pathologic mutations in the SURF1 gene. We conclude that DIA is a simple, fast and sensitive method for the determination of CIV in buccal cells and is suitable for the screening of CIV deficiency in non-invasively obtained material from children who are suspected of having mitochondrial disease.