Gene mutation may occur either in the parasite or in the host, which may be beneficial or harmful for each. As we previously discussed, part I covered causes and types of gene mutations as well as their relation(s) to or effect(s) on parasitic diseases; part II deals with parasite gene mutations. The most apparent manifestation is drug resistance especially with anti-malarial drugs for falciparum malaria. The majority of P. falciparum isolates are able to undergo gene mutations in genes encoding enzymes that control drug uptake. Parasite gene mutations are suggested to influence parasite virulence in toxoplasmosis and malignant malaria, and to have impact on the occurrence of malignancy in schistosomiasis and clonorchiasis. It is intended in the present review to present mechanism(s) of drug resistance due to parasite gene mutations, with special emphasis on anti-malarial drugs, albendazole, metronidazole, and other drugs used in treatment of African trypanosomiasis and toxoplasmosis. The review also presents other effects of parasite gene mutations on disease outcome and progress as well as occurrence of false diagnosis in falciparum malaria using ICTs utelizing histidine rich protein.