We present an algorithm to compute a higher dimensional analogue of modular polynomials. This higher dimensional analogue, the 'set of Hilbert modular polynomials', concerns cyclic isogenies of principally polarised abelian varieties with maximal real multiplication by a fixed totally real number field K0. We give a proof that this algorithm is correct, and provide practical improvements and an implementation for the 2-dimensional case with K0 = Q(√ 5). We also explain applications of this algorithm to point counting, walking on isogeny graphs, and computing class polynomials.