We genotyped pooled adult worms of Schistosoma mansoni from infected CF1, C57BL/6, BALB/c, and BALB/c interferon gamma knockout mice in order to investigate if mouse strain differences selected for parasite genotypes. We also compared differentiation in eggs collected from liver and intestines to determine if there was differential distribution of parasite strains in the vertebrate host that might account for any genotype selection. We found that mouse strains with differing immune responses did not differ in resistance to infection and did not select for parasite genotypes. S. mansoni genotypes were also equally distributed in tissues and there was no difference between adult and egg allele frequencies. Differing immune responses in these mouse strains does not significantly affect the degree or the nature of host resistance to schistosomes.