Cathepsin K, a papain-like cysteine protease, is highly expressed in osteoclasts and plays a critical role in bone resorption. Dysfunction of the enzyme leads to various skeletal abnormalities. The recent knowledge that the collagenolytic activity of cathepsin K depends on interactions with bone and cartilage-resident glycosaminoglycans (GAGs) may shed some light on diseases such as mucopolysaccharidoses (MPSs). MPSs are a group of lysosomal storage diseases characterized by the accumulation of GAGs in tissues including bone. Typical pathological features of these diseases include skeletal abnormalities such as dysostosis multiplex, short stature, and multiple irregularities in bone development. We describe how further investigation of the cathepsin K/GAG complexes could provide valuable insights into the bone pathology associated with MPS diseases. In this review, we discuss the inhibition of osteoclast function through altered activity of cathepsin K by GAGs and offer insight into a mechanism for the bone pathology seen in MPS patients.