Solid phase synthesis (SPS) of molecularly imprinted nanopolymers (nanoMIPs) represents an innovative method to prepare nanomaterials with tailor-made molecular recognition properties towards peptides and proteins. The synthesis of nanoMIPs by SPS usually involves a pre-polymerization formulation, where the cross-linker is invariably N,N'-methylen-bis-acrylamide (BIS). To date, the effect of cross-linkers on the binding properties of nanoMIPs prepared using cross-linkers other than BIS has never been reported. In this work, in order to investigate the effect of different cross-linkers in protein-imprinted nanoMIPs prepared by SPS, alongside BIS we considered other similar cross-linkers: N,N'-ethylene dimethacrylamide (EDAM), N,O-bis-methacryloylethanolamine (NOBE), ethylene glycol dimethacrilate (EDMA) and glycerol dimethacrylate (GDMA), replacing BIS with them in pre-polymerization mixtures. The synthetized nanoMIPs were homogeneous, with a polydispersity index of 0.24-0.30 and a mean diameter of 129-169 nm in water. The binding properties of the nanoMIPs were measured via equilibrium partition experiments with the template, rabbit IgG (RIgG), and the selectivity was evaluated with respect to bovine IgG (BIgG), bovine serum albumin (BSA) and hen egg lysozyme (LZM). The experimental results show that all the cross-linkers, with the exception of EDMA, endowed nanoMIPs with high binding affinities for the template (BIS: 16.0 × 106 mol-1 L, EDAM: 8.8 × 106 mol-1 L, NOBE: 15.8 × 106 mol-1 L, and GDMA: 12.8 × 106 mol-1 L), medium to high imprinting factors (BIS: 12.3, EDAM: 5.5, NOBE: 7.2, and GDMA: 11.6) and good selectivity towards other proteins but markedly dependent on the structure of the cross-linker, confirming the importance of the latter in the SPS of imprinted nanopolymers.