Karakilisa (Turkish for "black church"; also spelled Gharakilisa) may refer to:
- Ağrı, Turkey (Known as Karakilisa before 1923)
- Azatan, Armenia
- Gharibjanyan, Armenia
- Hartavan, Armenia
- Lernapar, Armenia
- Lerrnhovit, Armenia
- Sisian, Armenia
- Vanadzor, Armenia
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