The effect of thrombin on the metabolism of glycosaminoglycans (GAG) in cultured bovine aortic endothelial cells was investigated. Incubation of confluent endothelial cell cultures with thrombin at 1.0 NIH U/ml for 8 h and above caused a significant decrease in the accumulation of [S-35]sulfate-labeled GAG (S-35-GAG) in the cell layer. After a 24 h incubation, thrombin at 0.5 U/ml and above decreased the accumulation of S-35-GAG in both cell layer and medium. The percentage of S-35-GAG released into the medium during the last 3 h of 24 h incubation was significantly increased by thrombin. In thrombin- treated cell layer, both heparan sulfate and the other GAG was significantly decreased at the same degree. The incorporation of both [H-3]thymidine and [C-14]leucine was significantly increased by thrombin. Gabexate mesilate, a serine protease inhibitor, suppressed the thrombin inhibition. From these results, it was suggested that thrombin decreased S-35-GAG in the endothelial cell layer without a nonspecific damage of the cells through mainly an inhibition of GAG production and additionally a stimulation of GAG release.