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We study bi-Lagrangian structures (a symplectic form with a pair of complementary Lagrangian foliations, also known as para-K"ahler or K"unneth structures) on nilmanifolds of dimension less than or equal to 6. In particular, building on previous work of several authors, we determine which 6-dimensional nilpotent Lie algebras admit a bi-Lagrangian structure. In dimension 6, there are (up to isomorphism) 26 nilpotent Lie algebras which admit a symplectic form, 16 of which admit a bi-Lagrangian structure and 10 of which do not. We also calculate the curvature of the canonical connection of these bi-Lagrangian structures.

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