Background: Hypertensive African Americans have a ~50% response rate to thiazide diuretic treatment. This contributes to a high prevalence of uncontrolled high blood pressure. Here, we examined the role of the mitochondrial genome on thiazide diuretic treatment response in hypertensive African Americans enrolled in a clinical trial. Methods: Participants from the Antihypertensive and Lipid Lowering Treatment to Prevent Heart Attack Trial (ALLHAT, n= 4279) were genotyped using the Illumina Infinium Multi-Ethnic Beadchip. Haplotype groups were called using HaploGrep. We used a linear regression analysis to examine the association between mitochondrial haplogroups (L, M, and N) and changes in blood pressure and fasting glucose over six months and two years, respectively. Results: The analysis revealed a null association between mitochondrial haplogroups M and N versus L for each of the outcomes. In subgroup analysis, the L subclades L1, L2, and L3/L4 (versus L0) were each inversely associated with fasting glucose response (p < 0.05). Conclusions: This discovery analysis suggests the mitochondrial genome has a small effect on fasting glucose response, but not that of blood pressure, to thiazide diuretic treatment in African Americans.