We previously prepared and evaluated simple Eudragit S100 microparticles loaded with prednisolone (ES-MP) and Eudragit S100-coated chitosan-succinyl-prednisolone conjugate microparticles (Ch-MP/ES) in vitro. In this work, the effectiveness, toxic side effects (5 mg prednisolone (PD) eq/kg x 3 d, 10 mg PD eq/kg x 3 d), and pharmacokinetic characteristics (5 mg PD eq/kg) were examined using rats with colitis induced through 2,4,6-trinitrobenzenesulfonic acid. ES-MP did not change the efficacy or toxic side effects of PD, and this was attributed to incomplete delivery to the target site and prolonged systemic drug absorption by ES-MP. On the other hand, Ch-MP/ES promoted the efficacy of PD and ameliorated its toxic side effects due to better delivery to the target site, very slow drug release and the strong suppression of drug absorption. Only Ch-MP/ES, which markedly changed drug release characteristics, improved the in vivo features of PD.