Spermatozoon decondensation in the zygote leads to the initiation of chromatin remodeling during which protamines are removed and replaced with maternal histones. We hypothesize that damage to male germ cells induced by paternal exposure to cyclophosphamide may alter the timing of spermatozoal decondensation and the pattern of chromatin remodeling in the prepronuclear rat zygote. A specific order of sperm decondensation was observed, starting at the posterior end, proceeding to the ventral sides, followed by the tip, and finally the midbody region of the sperm head nucleus; subgroups of partially decondensed type a sperm nuclei were defined as types a1, a2, a3, and a4. Based on their frequencies relative to controls, paternal exposure to cyclophosphamide accelerated the timing of spermatozoal decondensation. Two distinct patterns of chromatin remodeling were observed for totally decondensed (type b) and recondensing (type c) sperm nuclei: H4K12ac showed a homogenous staining, whereas H3S10ph displayed a ring-like staining around the sperm nucleus; the distribution of these posttranslationally modified histones was not affected by cyclophosphamide exposure. In contrast, paternal cyclophosphamide treatment increased the number of gammaH2AX foci found in decondensing sperm nuclei. Small foci were significantly increased in type a2 and a3 nuclei, whereas a significant increase in the numbers of large foci was found in type b and c nuclei. This increase in gammaH2AX foci in the decondensing male genome suggests that damage recognition and repair pathways are initiated in prepronuclear rat zygotes. Thus, exposure of male rats to chronic low doses of cyclophosphamide accelerates spermatozoal decondensation and leads to the activation of gammaH2AX recognition of DNA damage in the male genome of the prepronuclear zygote.