Protamines are the major nuclear proteins condensing DNA in the sperm nucleus. One of their proposed functions is the protection of the genetic message delivered by the sperm. To date, evidence of their involvement in DNA protection has been obtained by correlating the protamine P1/P2 ratio, protamine concentrations, or chromomycin A3 staining with DNA fragmentation. However, a correlation of the absolute protamine/DNA content with the DNA fragmentation in sperm from the same infertile patients as assessed with the comet assay has not been studied. Protamine/DNA ratios were calculated after protamine and DNA extraction, electrophoresis, and gel quantification of the protamines and DNA quantification in the sperm samples of 66 infertile patients before (native sample) and after a 2-step discontinuous PureSperm density gradient centrifuged (DGC) selection of the sperm. DNA fragmentation was assessed using the alkaline comet assay. In DGC sperm, the total protamine/DNA, P1/DNA, and P2/DNA ratios all correlated inversely with DNA damage in sperm from infertile patients. The detection of this inverse correlation between protamine/DNA ratios and DNA damage in DGC sperm adds support to the hypothesis that defective protamination is related to DNA damage in the clinically relevant subpopulation of sperm from infertile men.