We study the Nekrasov partition function of the five dimensional U(N) gauge theory with maximal supersymmetry on R ^{^ 4} x S ^{^ 1} in the presence of codimension two defects. The codimension two defects can be described either as monodromy defects, or by coupling to a certain class of three dimensional quiver gauge theories on R ^{^ 2} x S ^{^ 1} . We explain how these computations are connected with both classical and quantum integrable systems. We check, as an expansion in the instanton number, that the aforementioned partition functions are eigenfunctions of an elliptic integrable many-body system, which quantizes the Seiberg-Witten geometry of the five-dimensional gauge theory.