Amorphous GexSe100−x (with x=10, 20 and 40 at%) alloys were prepared using the melt–quench technique. Two-dimensional Monte Carlo of the total pair distribution functions (MCGR) have been found and used to assemble the three-dimensional atomic configurations using the reverse Monte Carlo (RMC) method. The simulations are useful to compute the partial pair distribution functions and the partial structure factors of the studied glasses. The partial pair distribution functions indicate that the basic building units are GeSe4 and Ge2Se6 tetrahedral units in the Se-rich and Ge-rich glasses, respectively. Some of these tetrahedral units are connected by the homopolar units as confirmed by the bond angle distribution functions. The partial structure factors have shown that not only the homopolar Ge–Ge bonds, but also Se–Se bonds are behind the appearance of the first sharp diffraction peak (FSDP) in the total structure factor.