Summary We proposed hierarchical Poisson and binomial models for mapping multiple interacting quantitative trait loci (QTLs) for count traits in experimental crosses. We applied our methods to two counted reproductive traits, live fetuses (LF) and dead fetuses (DF) at 17 days gestation, in an F2 female mouse population. We treated observed number of corpora lutea (ovulation rate) as the baseline and the total trials in our Poisson and binomial models, respectively. We detected more than 10 QTLs for LF and DF, most having epistatic and pleiotropic effects. The epistatic effects were larger, involved more QTLs, and explained a larger proportion of phenotypic variance than the main effects. Our analyses revealed a complex network of multiple interacting QTLs for the reproductive traits, and increase our understanding of the genetic architecture of reproductive characters. The proposed statistical models and methods provide valuable tools for detecting multiple interacting QTLs for complex count phenotypes. Copyright © 2010 Cambridge University Press.