In the actual scenario of the search for further genetic susceptibility factors, a recent paper noted an SNP in the UCP2 gene as a multiple sclerosis (MS) risk factor. UCP2 is a member of the mitochondrial proton transport family, which uncouples proton entry in the mitochondrial matrix from ATP synthesis. mtDNA haplogroups are also associated with ATP production, and are linked with mitochondrial proton transport. In this work, we studied the UCP2 SNP and the mitochondrial haplogroups distribution in a Spanish MS population, with a population sub-group of Basque-origin patients. Our results confirm the link between UCP2 SNP and MS, and show a slight relation between this SNP and mitochondrial haplogroups.