The relationship between genetic alterations in mitochondrial DNA (mtDNA) and progressive motility (PR) and rapid progressive motility (grade A) of ejaculated human spermatozoa remains unclear. In this study, we explored the association between human mtDNA genotype and sperm PR and grade A by analyzing mtDNA copy number, loci, haplogroup, rearrangement, deletions, and duplications and sperm motility parameters. Human sperm mtDNA copy number, loci and haplogroups were not associated with human sperm motility PR or A grade. However, the cumulative frequency of human sperm mtDNA rearrangements (including deletions and duplications) in participants with high PR and grade A ratio was higher than in participants with low PR and grade A ratio. Additional studies are needed to understand the relationship between mtDNA genotypes, including deletions and duplications, and human sperm motility.