By demonstrating, in 1910, the presence of eggs of schistosomes in the kidneys of Egyptian mummies of the XXth Dynasty, Marc Armand Ruffer is considered as the founder of paleoparasitology. One century later, thanks to technologies derived from molecular biology, important advances have been made in the history of human parasitic diseases, especially in the fields of schistosomiasis, trypanosomiasis and leishmaniasis. For instance, it is probable that there was a common ancestor for the three main groups of schistosoma species which infect humans and animals today. Similarly, it is likely that South American and African trypanosomes arose from a common ancestral protozoa. This hypothesis is further sustained by the characterization of a protein (CCF-1 for Coelomic Cytolytic Factor-1), isolated from an annelid and which binds molecules expressed by two distinct species of trypanosoma. Lastly, recent data highlight the geographic distribution of various species of Leishmania in both the Old and the New World. Improvement in parasite phylogeny and systematics lead to a better understanding of the history of human parasitic diseases.