A facile polyelectrolyte complexation method for the preparation of both positively and negatively surface charged nanoparticles composed of chondroitin sulfate (ChS) and N-[(2-hydroxy-3-trimethylammonium)propyl]chitosan (HTCC) is reported. Production of ChS-HTCC nanoparticles with reverse zeta potential was easily controlled by varying the ChS/HTCC mass ratio. The encapsulation efficiency increased with the increase in initial FITC-BSA concentration in positively charged NPs and reached 75%. However, a maximum of 20% encapsulation efficiency was achieved in the case of negatively charged NPs. In vitro release studies of positively charged ChS-HTCC NPs showed a small burst effect followed by a continued and controlled release. Both charges of ChS-HTCC NPs showed no cytotoxicity in HUVECs. The confocal images showed that ChS-HTCC NPs of both charges can be incorporated and retained by the A549 cells. Flow cytometric analysis data demonstrated that ChS-HTCC NPs of both charges were detected in more than 80% of the A549 cells.