Throughout development and aging, human cells accumulate mutations resulting in genomic mosaicism and genetic diversity at the cellular level. Mosaic mutations present in the gonads can affect both the individual and the offspring and subsequent generations. Here, we explore patterns and temporal stability of clonal mosaic mutations in male gonads by sequencing ejaculated sperm. Through 300× whole-genome sequencing of blood and sperm from healthy men, we find each ejaculate carries on average 33.3 ± 12.1 (mean ± SD) clonal mosaic variants, nearly all of which are detected in serial sampling, with the majority absent from sampled somal tissues. Their temporal stability and mutational signature suggest origins during embryonic development from a largely immutable stem cell niche. Clonal mosaicism likely contributes a transmissible, predicted pathogenic exonic variant for 1 in 15 men, representing a life-long threat of transmission for these individuals and a significant burden on human population health. Display omitted •Mosaic variants are stably present across serial ejaculates•In sperm, unlike in blood, clonal mosaicism does not change with age•Mutational origins and temporal stability suggest an embryonic origin•Clonal sperm mosaicism is predicted to cause adverse outcomes in 1:300 concepti Sequencing of sperm from healthy men identifies clonal mosaic mutations that are likely embryonic in origin and unlike blood, stable over age. Further, clonal mosaic mutations likely contribute to transmissible pathogenic mutations in 1 of 15 men.