Quantitative analyses of anionic sites in the rat cartilage were performed by using post-embedding LR-Gold method with cationic colloidal gold (CCG) at different pH levels. Alteration of the pH levels affected the CCG staining patterns. The CCG particles were more observed at low pH levels, 1.0 and 2.5, than those at high pH 7.4. So, we quantitatively examined the superficial, intermediate and deep layers at pH 1.0. Morphometric analyses showed that CCG particles were increased from the superficial layer to the deep layer in both pericellular matrix (PM) and interterritorial matrix (IM). Moreover, they were more observed in PM than in IM. After chondroitinase ABC digestion, the CCG labeling was reduced in all matrices of the superficial and intermediate layers, though many CCG particles were still observed in PM of the deep layer. After hyaluronidase digestion, the CCG labeling was markedly reduced in the PM of the deep layer. These findings suggest that anionic sites in the cartilage matrix are detected by using the CCG only at low pH levels. In addition, the PM in the deep layer may consist of different components from those of the other two layers.