1. Intestine

Amebiasis (Amebic dysentery, Amebic colitis, Amebic appendicitis, Ameboma)
Entamoeba histolytica
Balantidiasis (Balantidial dysentery, Ciliary dysentery)
Balantidium coli
Cryptosporidiosis
Cryptosporidium parvum
Giardiasis
Giardia lamblia
Isosporiais
Isospora belli

2. Liver and biliary tree

Amebic liver abscess
Entamoeba histolytica
Giardiasis
Giardia lamblia
Visceral leishmaniasis (Kala-azar, Black fever, Black sickness, Dum-Dum fever, Leishmania donovani, L. infantum, L. chagasi)
Visceral Leishmania  

3. Heart and muscle

Chagas' disease (American trypanosomiasis)
Trypanosoma cruzi

4. Central nervous system (CNS)

African sleeping sickness
Mid-African trypanosomiasis
Trypanosoma gambiense
East-African trypanosomiasis
Trypanosoma rhodesiense
Amebic brain abscess
Entamoeba histolytica
Cerebral malaria
Plasmodium falciparum
Cerebral toxoplasmosis
Toxoplasma gondii
Chagas' disease (American trypanosomiasis)
Trypanosoma cruzi
Naegleria meningoencephalitis (Primary amebic meningoencephalitis)
Naegleria fowleri

5. Lung

Amebic lung abscess
Entamoeba histolytica
Pneumocystosis (Pneumocystis carinii pneumonia)
Pneumocystis carinii

6. Genitourinary organ

Trichomoniasis
Trichomonas vaginalis

7. Skin

Cutaneous amebiasis
Entamoeba histolytica
Cutaneous leishmaniasis (Leishmania tropica, L. major, L. mexicana, L. braziliensis,
L.  aethiopica, L.  amazonensis)
Cutaneous Leishmania

8. Eyes

Acanthamoeba keratitis  
Acanthamoeba species
Ocular toxoplasmosis (Toxoplasma chorioretinitis)
Toxoplasma gondii

9. Blood, bone marrow, lymphatics and spleen

African sleeping sickness (= African trypanosomiasis)
Trypanosoma gambiense, T. rhodesiense
Babesiosis
Babesia microti, B. bigemina
Chagas' disease (American trypanosomiasis)
Trypanosoma cruzi
Malaria
(1) Falciparum malaria (Malignant malaria)
Plasmodium falciparum
(2) Ovale malaria
Plasmodium ovale
(3) Quartan malaria
Plasmodium malariae
(4) Vivax malaria (= Tertian malaria)
Plasmodium vivax
Toxoplasmosis
Toxoplasma gondii
Viseral leishmaniasis (Kala-azar, Black fever, Black sickness, Dum-Dum fever, Leishmania donovani)
Visceral leishmania