Schistosomiasis is the most important helminth disease in the world from a public health perspective. S mansoni and S japonicum account for the majority of global intestinal schistosomiasis cases, and the pathogenesis is widely assumed to be fundamentally similar. However, the majority of research on schistosomiasis has been carried out on S mansoni and comparisons between the two species are rarely made. Here, we will discuss aspects of both older and recent literature where such comparisons have been made, with a particular focus on the pathological agent, the host granulomatous response to the egg. Major differences between the two species are apparent in features such as egg production patterns and cellular infiltration; however, it is also clear that even subtle differences in the cascade of various cytokines and chemokines contribute to the different levels of pathology observed between these two main species of intestinal schistosomiasis. A better understanding of such differences at species level will be vital when it comes to the development of new treatment strategies and vaccines.