Previous studies have identified glycosaminoglycans in gingival crevicular fluid (GCF) associated with a variety of clinical conditions, notably those involving bone resorptive activity. GCF was here collected from around teeth undergoing active orthodontic movement. Proteoglycan metabolites were purified from GCF by anion-exchange chromatography using fast performance liquid chromatography. Sulphated glycosaminoglycan was associated with the most highly anionic protein fractions IV, V and VI, and biochemical analysis was restricted to these fractions. Analysis included glycosaminoglycan content by cellulose acetate electrophoresis, molecular size by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting and amino acid analyses. Fraction IV contained hyaluronan (18.7%) and chondroitin sulphate (10.9%), fraction V heparan sulphate (29.5%) and chondroitin sulphate (19.6%) and fraction VI chondroitin sulphate only (21.3%). SDS-PAGE revealed two Coomassie blue bands in fraction V of 72 and 60 kDa and two further bands in fraction VI of 71 and 56 kDa. These proteoglycans appeared resistant to digestion by chondroitinase ABC or heparinase III, although the glycosaminoglycan chains underwent degradation after protein-core removal. The molecular mass and amino acid composition of the chondroitin sulphate proteoglycan fractions showed a close similarity to those of human alveolar bone proteoglycan. The presence of heparan sulphate proteoglycan in GCF in association with orthodontic movement is in accord with previous reports. The findings support the view that proteoglycans in GCF are 'biomarkers', notably those associated with active resorption of alveolar bone.