Genetic factors affecting spermatogenesis, sperm morphology, and chromatin structure in mice were estimated using a diallel cross of the inbred lines C3H/HeJ, C57BL/6J, DBA/2J, and BALB/cByJ. Flow cytometry of acridine orange stained cells was used to evaluate (i) proportions of testicular tetraploid, diploid, and haploid cells and (ii) nuclear chromatin structure of sperm, measured by resistance of chromatin to in situ acid denaturation, and quantified by the ratio of double- to single-stranded DNA (αt). Percent morphologically abnormal sperm was scored by light microscopy. Heterosis, line, maternal, and reciprocal effects, and general and specific combining abilities were estimated for body and testis weights, testicular cell proportions, sperm αt values, and percent abnormal sperm. Heterosis was important for testis weight, αt values, and percent abnormal sperm. Inbreds varied in body and testicular weights, αt values, and percent abormal sperm. Significant maternal effects were noted for several traits but could be due to sex-linked (X or Y) factors, since maternal and sex-linked effects were confounded. Although a high positive correlation existed between αt values and percent abnormal sperm, the proportion of sperm with altered chromatin structure, measured by FCM, was generally much lower than proportion of morphologically abnormal cells.Key words: mouse, spermatogenesis, chromatin structure, flow cytometry, diallel.