Humans show 13.7% ancient SNVs exceeding neutral expectations across models. Ancient deletions comprise 8.8% of polymorphisms, predating 700kya human-archaic split. Ancient deletions exhibit higher stdβ2 balancing selection scores than non-ancient in YRI, CEU, CHB. Common ancient deletions show 4.2-fold enrichment for exonic plus GWAS-associated traits. Ancient deletions 12.5-fold enriched for inflammatory traits, 2.8-fold for metabolism. Deletions more deleterious than SNVs, purged faster by negative selection. Ancient deletions median age 1 million years, 15% over 2 million. Overdominance rare – variable spatial/temporal selection drives persistence. Ancient deletions cause whole-gene losses in immune/metabolic families like LCE3, UGT2B. Ancient deletions alter HLA expression, isoforms in GHR, SIRPB1, CYP3A43. Longest ancient deletions excess despite negative selection, prime balancing targets. 50% of functional exonic GWAS deletions are ancient. Ancient polymorphisms shared across YRI, CEU, CHB regardless of race. Balancing selection underappreciated for common human variation.