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Hydrocephalus is a genetically and phenotypically heterogenous condition with complex etiology. Ciliary dysfunction has been shown to play a role, either through interference with signaling functions in primary cilia, cerebrospinal fluid flow by motile cilia, or both. Ciliary function is highly energy-dependent, consequently, variation in mitochondrial OXPHOS function might be a susceptibility factor for hydrocephalus. Furthermore, familial hydrocephalus exhibits preferential maternal inheritance. Mitochondrial DNA (mtDNA) haplogroups, have been associated with different characteristics of OXPHOS function as well as susceptibility to autism spectrum disorders, a frequent co-morbidity of hydrocephalus. This nested case-cohort study, a substudy of the iPSYCH study, used mtDNA data from 191 hydrocephalus cases and 24,831 population controls and found no association between hydrocephalus and any mtDNA haplogroup. Likewise, the distribution of European macro-haplogroups, HV, JT, and UK, did not differ between 172 hydrocephalus cases and 21,850 population controls. Thus, mtDNA haplogroups are not susceptibility factors for hydrocephalus.