DNA is one of the most essential molecules in organisms, containing all the information necessary for organisms to live. It replicates and provides a mechanism for heredity and evolution. Various events cause the degradation of DNA into nucleotides. DNA also has a darker side that has only recently been recognized; DNA that is not properly degraded causes various diseases. In this review, we discuss four deoxyribonucleases that function in the nucleus, cytosol, and lysosomes, and how undigested DNA causes such diseases as cancer, cataract, and autoinflammation. Studies on the biochemical and physiological functions of deoxyribonucleases should continue to increase our understanding of cellular functions and human diseases.