Mitochondrial disease (MD) is diagnosed by muscle biopsy, including light and electron microscopy (EM), respiratory chain enzyme analysis (RCEA) and genetic studies. As EM and RCEA are costly and time-consuming, we compared muscle biopsies performed during January to June of 2004 and 2005. 34 cases from 2004 and 30 from 2005 were examined. Clinically suspected MD made up one third of total biopsy requests (32.6% in 2004, 36% in 2005). Biopsies were reviewed by a pathologist and medical records reviewed by a clinician blinded to the pathological analysis. In the majority of cases, RCEA (88% in 2004, 83% in 2005) showed no supportive evidence of MD. In a small number of cases without histological evidence of MD (2 in 2004, 3 in 2005), RCEA was abnormal. EM did not provide additional diagnostic information. Chronic progressive external ophthalmoplegia was the only clinical predictor of a positive biopsy. There was no statistical difference in age, sex, duration of symptoms, site of disease or referring clinician between biopsy positive and negative cases. We propose that in cases with suspected MD, the combination of histological examination and RCEA provides maximal diagnostic information. EM offers no additional diagnostic yield and should not be routinely performed.