Friedreich ataxia (FRDA) is a neurodegenerative disease caused by mutations in the frataxin (FXN) gene, resulting in reduced expression of the mitochondrial protein frataxin. While there currently is no cure for FRDA, our increasing understanding of the pathophysiology of disease has led to a surge in the development of potential treatments. As a result, there is a growing need for biological markers of disease progression and patient response to therapeutic intervention. In this thesis, we developed and validated a lateral flow “dipstick” immunoassay for the measurement of frataxin protein in multiple peripheral cell types. We measured significant differences in frataxin levels between controls, carriers, and FRDA patients, and found correlations between frataxin levels and GAA1 repeat length and age of onset. We then compared the utility of the dipstick assay as a population screening and diagnostic tool to a separate, Luminex xMAP-based immunoassay, and discuss the advantages and disadvantages of each assay in different clinical settings. The dipstick assay showed utility in a variety of clinical applications, including preliminary diagnosis of atypical FRDA patients, analysis of longitudinal frataxin measurements, correlations with changes in neurological severity, patient response to HDAC inhibitor treatment, response to chemotherapy in an FRDA case with comorbid osteosarcoma, and assessment of HDAC and SIRT gene polymorphisms on frataxin protein expression. Finally, we used Stable Isotope Labeling with Essential nutrients in Cell culture (SILEC) methodology to assess metabolic changes in transfected cells as well as primary fibroblasts and platelets isolated from FRDA patients. Using SILEC internal standards, we found that acetyl-CoA:succinyl-CoA ratios were significantly decreased in FRDA patients compared to controls, consistent with in vitro siRNA knockdown models of frataxin. Changes in CoA profiles, coupled with isotopic tracer analysis using [U-13C6]-glucose and [U-13C16]-palmitic acid, provided us with further insight into possible metabolic dysfunction in FRDA. Taken together, the results from this thesis show utility for frataxin measurements from peripheral tissues as a biomarker, and potentially provide researchers with a novel set of markers to assess metabolic dysfunction in unaffected tissues, not just in FRDA, but in any mitochondrial disorder.