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 establish 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. Schistosoma mansoni egg allele frequencies were also equally distributed in tissues and the difference between adult and egg allele frequencies was negligible.