We examined the rate and nature of mitochondrial DNA (mtDNA) mutations in humans using sequence data from 64,806 contemporary Icelanders from 2,548 matrilines. Based on 116,663 mother-child transmissions, 8,199 mutations were detected, providing robust rate estimates by nucleotide type, functional impact, position, and different alleles at the same position. We thoroughly document the true extent of hypermutability in mtDNA, mainly affecting the control region but also some coding-region variants. The results reveal the impact of negative selection on viable deleterious mutations, including rapidly mutating disease-associated 3243A>G and 1555A>G and pre-natal selection that most likely occurs during the development of oocytes. Finally, we show that the fate of new mutations is determined by a drastic germline bottleneck, amounting to an average of 3 mtDNA units effectively transmitted from mother to child. Display omitted •Detection of 8,199 mutations in 116,663 mother-child mtDNA transmissions•Position and allele-specific mutation rates reveal asymmetric hypermutability•Evidence for both pre- and post-natal selection against mtDNA variants•Children inherit effectively only ∼3 units of mtDNA from their mothers This large-scale pedigree study of human mtDNA mutations reveals substantial selection against deleterious variants both before and after birth, characterizes extensive differences in mutability by position and allele, and shows that children only inherit around 3 units of mtDNA from their mothers.