We construct a separation of variables for the classical n-particle Ru
ijsenaars system (the relativistic analog of the elliptic Calogero-Mos
er system). The separated coordinates appear as the poles of the prope
rly normalised eigenvector (Baker-Akhiezer function) of the correspond
ing Lax matrix. Two different normalisations of the BA functions are a
nalysed. The canonicity of the separated variables is verified with th
e use of the r-matrix technique. The explicit expressions for the gene
rating function of the separating canonical transform are given in the
simplest cases n = 2 and n = 3. Taking the nonrelativistic limit we a
lso construct a separation of variables for the elliptic Calogero-Mose
r system.