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The following subdivisions are active at the Institute of Baltic Region History and Archaeology of Klaipėda University:

  1. Centre for Evangelical Theology, founded in 1992; part of the institute since 2014;
  2. Underwater Research Centre, founded in 2003. Headed by Elena Pranckėnaitė;
  3. Osteological Material Research Laboratory, founded in 2010. Headed by Linas Daugnora;
  4. Experimental Archaeology and Traceology Laboratory, founded in 2011. Headed by Tomas Rimkus;
  5. Centre for Conservation and Restoration, founded in 2020. Headed by Akvilė Poškienė.