Modern humans show 47 archaic segments overlapping reproduction genes at 40%+ frequencies, 20 times higher than average archaic DNA. Africans have under 1% archaic variants matching Neanderthals or Denisovans. Non-Africans average 2% Neanderthal DNA and up to 5% Denisovan in Oceanians. 11 core haplotypes overlap 15 reproduction genes with selection signals. Three core haplotypes positively selected: AHRR in Finns, FLT1 in Peruvians, PNO1-PPP3R1 in Chinese Dai. AHRR haplotype from Chagyrskaya Neanderthal rapidly expanded in Finns after 10,000 years ago. 327 archaic alleles genome-wide significant for traits, 308 are eQTLs regulating 176 genes. 81% core haplotype eQTLs regulate genes in ovaries, prostate, testes, uterus, vagina. Archaic alleles on chromosome 2 protect against prostate cancer in Asians and Europeans. Genes enriched in developmental pathways, embryo development, cancer metabolism. Archaic PGR haplotype reduces miscarriages and pregnancy bleeding in Europeans. Selection is recent, regional standing selection favoring archaic haplotypes in specific populations. FLT1 archaic alleles linked to preeclampsia and embryo death risks. AHRR associated with micropenis, infertility under pollutants, endometriosis. Non-African haplotypes cluster near archaic donors, distant from African haplotypes. Archaic eQTLs overrepresented in testis expression versus random variants.