In this paper, we study the relative controllability of linear difference equations with multiple delays in the state by using a suitable formula for the solutions of such systems in terms of their initial conditions, their control inputs, and some matrix-valued coefficients obtained recursively from the matrices defining the system. Thanks to such formula, we characterize relative controllability in time $T$ in terms of an algebraic property of the matrix-valued coefficients, which reduces to the usual Kalman controllability criterion in the case of a single delay. Relative controllability is studied for solutions in the set of all functions and in the function spaces $L^p$ and $\mathcal C^k$. We also compare the relative controllability of the system for different delays in terms of their rational dependence structure, proving that relative controllability for some delays implies relative controllability for all delays that are "less rationally dependent" than the original ones, in a sense that we make precise. Finally, we provide an upper bound on the minimal controllability time for a system depending only on its dimension and on its largest delay.