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There are 18 referenced airports for this country:
| Name | ICAO Code | IATA Code |
| Amari | EEEI | |
| Haapsalu | EEHU | |
| Johvi | EEJI | |
| Kärdla | EEKA | KDL |
| Kihnu | EEKU | |
| Kuressaare | EEKE | URE |
| Narva | EENA | |
| Nurmsi | EENI | |
| Pärnu | EEPU | EPU |
| Piirisaar | EEPR | |
| Rapla | EERA | |
| Ridali | EERI | |
| Ruhnu | EERU | |
| Tallinn Ulemiste | EETN | TLL |
| Tapa | EETA | |
| Name | ICAO Code | IATA Code |
| Tartu Raadi | EETR | |
| Tartu Ulenurme | EETU | TAY |
| Viljandi | EEVI |
