The immune system is central to the development and resolution of complex diseases that still challenge modern therapeutic medicine such as autoimmunity and cancer. Recent blunt immune system manipulations, such as systemic monoclonal antibodies, have shown great promise in subsets of these conditions. But more controlled therapeutic manipulation of immune cell function must involve the ultimate source of that functionality, the genome itself. First, we manipulated immune cell genomes by extending high efficiency gene knockout technologies to primary human and mouse T, B, and NK cells using CRISPR/Cas9 RNP electroporation. Yet only so much therapeutic potential can be expected from removing endogenous genetic instructions. The ability to target large amounts of new genetic material to specific sites in immune cell genomes offers a potentially infinite number of therapeutic modifications. Second, we thus present non-viral genome targeting, a simple high efficiency method for the targeted integration of large (>3 kB) sequences of DNA into diverse primary human immune cell types. We applied non-viral genome targeting in three ways: the correction of a monogenic autoimmune mutation in patient cells; the replacement of T cell’s endogenous TCR with a new specificity, such as for a common melanoma antigen; and the integration of synthetic DNA sequences into endogenous genetic loci for a new class of therapeutic cell modifications, termed Genetically Engineered Endogenous Proteins. Finally, we extended non-viral genome targeting to develop a robust targeted pooled knockin method, allowing for libraries of large DNA modifications integrated into endogenous genomic sites to be rapidly screened for their functional effects on primary human T cells. Overall, human immune cell specificity and function can now be engineered without costly viral vectors or random integrations through non- viral genome targeting, opening the next chapter in immune cell therapies for cancer and autoimmunity. And beyond its therapeutic potential, large scale modifications of the endogenous genome will enable new avenues of biology exploring the evolutionary choices, trade offs, and paths untaken, that comprise our collective genome.