We describe an ex vivo rat infection model to study protective immunity against Fasciola hepatica at the gut level. An exact number of newly excysted juveniles (NEJs) was injected into a gut segment with an intact blood supply and which was still attached to a live anaesthetized rat. NEJs that penetrated the gut wall during the following 6 h were recovered from a beaker filled with medium and were counted under a microscope. This infection model was validated and enabled us to exactly quantify the infection dose whilst at the same time exactly quantifying the number of NEJs penetrating the gut wall. The mean sum of NEJs that migrated through the gut wall into the beaker (peritoneal fraction), plus NEJs that remained in the gut wall and the gut lumen was 87% of the infective dose (±3.6% SEM; n=18). The function of the ex vivo segments was well-preserved, as demonstrated by only minor leakage of an inert liquid marker. The ex vivo model enabled us to measure protection against F. hepatica at the gut level. In naive rats 52% (±2.4% SEM; n=40) of the injected NEJs penetrated the gut wall, whereas in previously infected rats only 12% (±1.8% SEM; n=40) were able to do so, irrespective of the infection dose. Thus, when rats were orally primed, the migration of NEJs through the gut wall was 77% less than the migration in naive rats. We conclude that the ex vivo model should be valuable in studies of the induction and expression of protective immunity against F. hepatica in the intestine, and will aid in development and optimization of vaccines.