The mouse type 2 Alu (B2) sequence was detected in both DNAs of Schistosoma mansoni and S. japonicum except for the cercarial stage by the polymerase chain reaction (PCR). Using several kinds of mouse STMS (sequence tagged microsatellite site) primer sets, PCR products related to the host were found in the DNAs of S. mansoni as well as of S. japonicum. Products could be detected only in the DNA of S. japonicum using certain STMS primer sets. The fact that no products could be amplified from the DNAs of both parasites when other kinds of STMS primer sets were used suggests unequal incorporation of the host DNA into the schistosomes. Furthermore, the sequence of the N-terminal domain of H-2, the mouse major histocompatibility complex (MHC), was detected in the DNAs from S. mansoni miracidium, male adult and S. japonicum adults, whereas the sequence of the C2 domain of H-2 was found only in the DNAs of S. japonicum adults. This evidence that host DNA sequences, including the class I MHC, exist heterogeneously in the DNAs of schistosomes might provide an important insight for further understanding of host-parasite immune interactions.