| algeria | | encephalitozoon cuniculi | species | 3 | 0 |
| anguilla | | encephalitozoon cuniculi | species | 0 | 1 |
| australia | | encephalitozoon cuniculi | species | 1 | 0 |
| australia | | encephalitozoon intestinalis | species | 1 | 0 |
| australia | new south wales | encephalitozoon intestinalis | species | 0 | 1 |
| australia | victoria | encephalitozoon cuniculi | species | 0 | 1 |
| australia | western australia | encephalitozoon cuniculi | species | 0 | 1 |
| austria | | encephalitozoon cuniculi | species | 4 | 0 |
| austria | vienna | encephalitozoon cuniculi | species | 0 | 1 |
| austria | vorarlberg | encephalitozoon cuniculi | species | 0 | 1 |
| brazil | sao paulo | encephalitozoon cuniculi | species | 0 | 1 |
| canada | | encephalitozoon intestinalis | species | 1 | 0 |
| canada | | encephalitozoon pogonae | species | 1 | 0 |
| central african republic | sangha-mbaere | encephalitozoon cuniculi | species | 0 | 1 |
| china | | encephalitozoon cuniculi | species | 5 | 0 |
| china | | encephalitozoon hellem | species | 2 | 0 |
| china | | encephalitozoon intestinalis | species | 5 | 0 |
| china | beijing | encephalitozoon cuniculi | species | 0 | 1 |
| china | chongqing | encephalitozoon hellem | species | 2 | 0 |
| china | hunan | encephalitozoon cuniculi | species | 0 | 1 |
| china | liaoning | encephalitozoon cuniculi | species | 0 | 1 |
| colombia | antioquia department | encephalitozoon intestinalis | species | 0 | 1 |
| czech republic | | encephalitozoon cuniculi | species | 6 | 0 |
| czech republic | prague city | encephalitozoon intestinalis | species | 0 | 1 |
| democratic republic of the congo | kinshasa city | encephalitozoon intestinalis | species | 0 | 1 |
| egypt | | encephalitozoon cuniculi | species | 1 | 0 |
| egypt | alexandria governorate | encephalitozoon cuniculi | species | 0 | 2 |
| egypt | beheira governorate | encephalitozoon cuniculi | species | 0 | 1 |
| ethiopia | addis ababa | encephalitozoon intestinalis | species | 0 | 1 |
| germany | | encephalitozoon cuniculi | species | 2 | 0 |
| germany | berlin | encephalitozoon cuniculi | species | 0 | 1 |
| germany | berlin | encephalitozoon intestinalis | species | 0 | 1 |
| guatemala | guatemala department | encephalitozoon intestinalis | species | 0 | 1 |
| haiti | | encephalitozoon cuniculi | species | 0 | 1 |
| indonesia | | encephalitozoon cuniculi | species | 1 | 0 |
| indonesia | south sulawesi province | encephalitozoon cuniculi | species | 1 | 0 |
| iran | | encephalitozoon cuniculi | species | 19 | 0 |
| iran | | encephalitozoon hellem | species | 15 | 0 |
| iran | | encephalitozoon intestinalis | species | 34 | 0 |
| iran | east azerbaijan province | encephalitozoon intestinalis | species | 1 | 0 |
| iran | tehran province | encephalitozoon cuniculi | species | 0 | 1 |
| iran | tehran province | encephalitozoon hellem | species | 0 | 1 |
| iran | tehran province | encephalitozoon intestinalis | species | 0 | 1 |
| ireland | | encephalitozoon cuniculi | species | 2 | 0 |
| ireland | | encephalitozoon intestinalis | species | 1 | 0 |
| israel | jerusalem district | encephalitozoon cuniculi | species | 0 | 1 |
| italy | veneto region | encephalitozoon cuniculi | species | 0 | 1 |
| japan | | encephalitozoon cuniculi | species | 2 | 0 |
| japan | | encephalitozoon pogonae | species | 1 | 0 |
| japan | hokkaido prefecture | encephalitozoon cuniculi | species | 0 | 1 |
| japan | tokyo prefecture | encephalitozoon cuniculi | species | 1 | 0 |
| malaysia | pahang | encephalitozoon intestinalis | species | 0 | 2 |
| mali | bamako region | encephalitozoon intestinalis | species | 0 | 1 |
| netherlands | north holland province | encephalitozoon cuniculi | species | 0 | 1 |
| netherlands | north holland province | encephalitozoon hellem | species | 0 | 1 |
| netherlands | north holland province | encephalitozoon intestinalis | species | 0 | 1 |
| niger | niamey region | encephalitozoon intestinalis | species | 0 | 1 |
| nigeria | lagos | encephalitozoon intestinalis | species | 0 | 1 |
| pakistan | | encephalitozoon intestinalis | species | 4 | 0 |
| poland | | encephalitozoon cuniculi | species | 28 | 0 |
| poland | | encephalitozoon hellem | species | 7 | 0 |
| poland | | encephalitozoon intestinalis | species | 2 | 0 |
| poland | | encephalitozoon sp. | species | 2 | 0 |
| poland | greater poland province | encephalitozoon hellem | species | 4 | 0 |
| poland | greater poland province | encephalitozoon intestinalis | species | 3 | 0 |
| russia | saint petersburg | encephalitozoon cuniculi | species | 0 | 2 |
| russia | saint petersburg | encephalitozoon hellem | species | 0 | 1 |
| russia | saint petersburg | encephalitozoon intestinalis | species | 2 | 1 |
| rwanda | | encephalitozoon cuniculi | species | 2 | 0 |
| spain | | encephalitozoon intestinalis | species | 1 | 0 |
| spain | canary islands | encephalitozoon cuniculi | species | 2 | 0 |
| spain | galicia | encephalitozoon intestinalis | species | 0 | 1 |
| spain | madrid | encephalitozoon cuniculi | species | 0 | 1 |
| spain | madrid | encephalitozoon intestinalis | species | 0 | 1 |
| spain | murcia | encephalitozoon cuniculi | species | 0 | 1 |
| spain | murcia | encephalitozoon hellem | species | 0 | 1 |
| spain | murcia | encephalitozoon intestinalis | species | 0 | 1 |
| switzerland | zurich region | encephalitozoon cuniculi | species | 0 | 1 |
| switzerland | zurich region | encephalitozoon hellem | species | 31 | 0 |
| taiwan | | encephalitozoon cuniculi | species | 0 | 1 |
| tanzania | zanzibar central/south region | encephalitozoon cuniculi | species | 0 | 1 |
| tanzania | zanzibar central/south region | encephalitozoon hellem | species | 0 | 1 |
| turkey | | encephalitozoon cuniculi | species | 1 | 0 |
| turkey | | encephalitozoon hellem | species | 2 | 0 |
| turkey | | encephalitozoon intestinalis | species | 3 | 0 |
| turkey | samsun province | encephalitozoon intestinalis | species | 1 | 0 |
| uganda | | encephalitozoon cuniculi | species | 3 | 0 |
| united kingdom | | encephalitozoon cuniculi | species | 1 | 0 |
| united kingdom | england | encephalitozoon cuniculi | species | 0 | 3 |
| united kingdom | england | encephalitozoon intestinalis | species | 0 | 1 |
| united kingdom | scotland | encephalitozoon cuniculi | species | 0 | 2 |
| united kingdom | wales | encephalitozoon cuniculi | species | 0 | 1 |
| united states | | encephalitozoon cuniculi | species | 3 | 0 |
| united states | | encephalitozoon hellem | species | 2 | 0 |
| united states | | encephalitozoon intestinalis | species | 5 | 0 |
| united states | | encephalitozoon pogonae | species | 2 | 0 |
| united states | florida | encephalitozoon cuniculi | species | 0 | 1 |
| united states | georgia | encephalitozoon cuniculi | species | 0 | 1 |
| united states | iowa | encephalitozoon cuniculi | species | 0 | 1 |
| united states | louisiana | encephalitozoon cuniculi | species | 0 | 1 |
| united states | maryland | encephalitozoon cuniculi | species | 0 | 1 |
| united states | maryland | encephalitozoon hellem | species | 0 | 1 |
| united states | maryland | encephalitozoon intestinalis | species | 0 | 2 |
| united states | massachusetts | encephalitozoon intestinalis | species | 0 | 1 |
| united states | new jersey | encephalitozoon cuniculi | species | 0 | 1 |
| united states | oklahoma | encephalitozoon cuniculi | species | 0 | 1 |
| united states | oklahoma | encephalitozoon hellem | species | 0 | 1 |
| united states | texas | encephalitozoon cuniculi | species | 0 | 1 |
| united states | texas | encephalitozoon hellem | species | 0 | 1 |
| united states | virginia | encephalitozoon cuniculi | species | 0 | 1 |
| venezuela | zulia | encephalitozoon intestinalis | species | 0 | 1 |
| vietnam | ha noi city | encephalitozoon intestinalis | species | 0 | 1 |
| zambia | southern province | encephalitozoon intestinalis | species | 0 | 1 |