Late thrombosis and neointima proliferation after paclitaxel-eluting stents implanting may be related to delayed endothelial cells (ECs) regeneration. This study was to investigate whether mesenchymal stem cells (MSCs) seeding can accelerate endothelial repair and attenuate late smooth muscle cells (SMCs) proliferation after paclitaxel intervention. An ex vivo model of endothelium repair was developed in which rabbit smooth muscle cells were inoculated in the upper chamber and rabbit endothelial cells/human mesenchymal stem cells in the lower chamber of a co-culture system. Paclitaxel (10 nmol/L, 20 min) inhibited smooth muscle cell growth of the confluent endothelial cell group during the observed period. However, increased smooth muscle cells growth was observed in the proliferative endothelial cells group 10 days after paclitaxel intervention. Mesenchymal stem cell seeding inhibited late smooth muscle cell growth incompatible with the effect of proliferative endothelial cells. However, no inhibition on smooth muscle cell growth was observed with mesenchymal stem cell seeding in comparison to the effect of confluent endothelial cells. No vWF but Flk-1 protein was observed in the 25.71% of mesenchymal stem cells after having been co-cultured with rabbit endothelial cells for 5 days. These results indicate that late smooth muscle cell proliferation is closely related to the delayed endothelial cells regeneration after paclitaxel application. Mesenchymal stem cell seeding partly attenuates the late smooth muscle cell proliferation. Mesenchymal stem cells co-cultured with mature endothelial cells have the ability to differentiate toward endothelial cells.