Clinically used scaffolds are suboptimal in regenerating the highly oriented meniscus fiber structure in full meniscal defects. The objective of this study was to test whether anisotropic porous scaffolds with channels resulted in a more meniscus like matrix organization compared to isotropic porous scaffolds. Isotropic polyurethane scaffolds were made via standard solvent leaching techniques. Anisotropic porous scaffolds with channels were made via modified thermal induced phase separation. Both scaffold types were analyzed with light microscopy, scanning electron microscopy and computed nano-tomography. Finally, isotropic and anisotropic scaffolds were bilaterally and subcutaneously implanted on the back of 32 Wistar rats for 1, 4, 8 and 24 weeks to assess tissue ingrowth and matrix organization. Isotropic scaffolds had a pore diameter of 35±14.7 μm and a degree of anisotropy of 0.18, while anisotropic scaffolds had a channel diameter of 20±6.0 μm and a degree of anisotropy of 0.39. After implantation full tissue ingrowth was achieved after 8 and 24 weeks for isotropic and anisotropic, respectively. Isotropic scaffolds had a random tissue infiltration with unorganized collagen deposition, whereas anisotropic scaffolds showed tissue infiltration and collagen alignment in the direction of the channels. Anisotropic scaffolds resulted in a matrix organization that resembled the tissue in the vascularized zone of the meniscus, while isotropic scaffolds resembled the tissue in the avascular zone of the meniscus.