Site-specific and depth-dependent properties of cartilage were implemented within a finite element (FE) model to determine if compositional or structural changes in the tissue could explain site-specific alterations of chondrocyte deformations due to cartilage loading in rabbit knee joints 3 days after a partial meniscectomy (PM). Depth-dependent proteoglycan (PG) content, collagen content and collagen orientation in the cartilage extracellular matrix (ECM), and PG content in the pericellular matrix (PCM) were assessed with microscopic and spectroscopic methods. Patellar, femoral groove and samples from both the lateral and medial compartments of the femoral condyle and tibial plateau were extracted from healthy controls and from the partial menisectomy group. For both groups and each knee joint site, axisymmetric FE models with measured properties were generated. Experimental cartilage loading was applied in the simulations and chondrocyte volumes were compared to the experimental values. ECM and PCM PG loss occurred within the superficial cartilage layer in the PM group at all locations, except in the lateral tibial plateau. Collagen content and orientation were not significantly altered due to the PM. The FE simulations predicted similar chondrocyte volume changes and group differences as obtained experimentally. Loss of PCM fixed charge density (FCD) decreased cell volume loss, as observed in the medial femur and medial tibia, whereas loss of ECM FCD increased cell volume loss, as seen in the patella, femoral groove and lateral femur. The model outcome, cell volume change, was also sensitive to applied tissue geometry, collagen fibril orientation and loading conditions.