Chitosan (CS) nanoparticles of dorzolamide hydrochloride (Dorzo) and pramipexole hydrochloride (Prami) were prepared by the ionic gelation method and their in vitro properties were studied. The long-term objective is the development of efficient ocular formulations for Dorzo and efficient oral formulations for Prami. The particle size of nanoparticles was affected by the CS/drug ratio whereas it was not affected by the type of drug (Dorzo or Prami). Drug association efficiency to the nanoparticles did not appear to correlate with the drug/CS ratio whereas the loading capacity tended to fall with increasing drug proportion. Based on WAXD data, Dorzo was dispersed in the nanoparticles in crystalline form, probably due to the weak interaction developed between Dorzo and CS/TPP matrix as FT-IR data indicated. In contrast, WAXD and step-scan DSC data indicated that Prami formed a molecular dispersion within the nanoparticles. This was probably due to the potent interactions developed between Prami and CS/TPP matrix, as FT-IR data revealed. The nanoparticles exhibited mucoadhesive properties which diminished with increasing drug content. Sustained in vitro drug release was observed with the Dorzo-loaded CS nanoparticles in PBS (pH 7.4) and with the Prami-loaded CS nanoparticles in simulated intestinal fluid. The results obtained in this study suggest that the Dorzo-loaded CS nanoparticles and the Prami-loaded CS nanoparticles could be further evaluated for the controlled ocular delivery of Dorzo and the controlled oral delivery of Prami, respectively.