Background Successful periodontal regeneration depends on the migration, proliferation and differentiation of periodontal ligament cells in periodontal defects. The total protein content and the ultrastructure demonstrate the metabolizability and activity of periodontal ligament cells. This study was conducted to observe the effects of Shuanghuangbu, a mixture of medicinal herbs, on the total protein content and the ultrastructure of human periodontal ligament cells. Methods Periodontal ligament cells were grown to confluence and then cultured in Dulbecco' s modified eagle medium (DMEM) supplemented with Shuanghuangbu over the concentration range of 0 to 1000 mug/ml. The total protein content in cultured cells was determined by using Coommasie brilliant blue technique. Periodontal ligament cells were incubated in 0 and 100 mug/ml Shuanghuangbu decoction for 5 days, then observed through transmission electron microscope. Results The total protein content of human periodontal ligament cells increased in each experiment group added 10 - 1000 mug/ml Shuanghuangbu respectively, and the effect of 100 mug/ml was excellent. Under the transmission electron microscope, there were more rough endoplasmic reticulums and mitochodrias in the experiment group than those in the control group. Conclusion Shuanghuangbu stimulates the protein synthesis of human periodontal ligament cells and improves human periodontal ligament cells' metabolizability and activity.