Incorporation of inorganic nanoparticles into polymer matrices is a method to increase the hydrophilicity and to reduce fouling in polymer membranes. Among different types of inorganic nanoparticles employed in mixed matrix membranes, TiO₂ and ZnO play significant role in their unique physical and chemical properties. In the present work, the effect of TiO₂ and ZnO nanoparticles on the structure and fouling behavior of polyethylene membranes was studied. High density polyethylene (HDPE) was used as polymer and TiO₂ and ZnO were of nanoparticle size. Thermally induced phase separation method was used to prepare membranes and different characterization methods including (field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDX), atomic force microcopy (AFM), contact angle, pure water flux and mean pore radius measurements were acquired to evaluate the structure and surface of the membranes. Moreover, the performance and fouling of the membranes were studied by separating 1 wt% collagen protein solution. The results of FESEM images showed that all the membranes had leafy structure, indicating solid-liquid phase separation during membrane preparation. The results of TEM and EDX confirmed the presence of nanoparticles in the membranes. Based on the Wenzel model, contact angle of the membranes was not reduced by increasing the content of hydrophilic nanoparticle due to increased surface roughness. However, pure water flux of the membranes increased as the content of nanoparticles increased. Finally, it was shown that the incorporation of nanoparticles increased reversible fouling, flux recovery and fouling resistance of the membranes in separation of collagen protein solution due to the antifouling properties of TiO₂ and ZnO nanoparticles.