Tacrolimus proved its distinct mitigating potential in the treatment of inflammatory bowel disease (IBD). Due to the risk for severe adverse effects and to achieve increased efficiency and tolerability, a selective delivery to the site of inflammation is of interest. Tacrolimus nanoparticles (NP) were tested for their efficiency in local treatment of inflamed bowel tissue in IBD. Drug loaded NP were prepared from either biodegradable poly(lactide-co-glycolide) (PLGA) or pH-sensitive Eudragit P-4135F by using a simple oil/water emulsification method. Tests on the therapeutic effect were conducted using dextran sulfate model colitis in mice receiving tacrolimus formulations daily for 12 days. Clinical activity score and myeloperoxidase activity decreased while colon length increased significantly after administration of all tacrolimus containing formulations. Oral NP formulations were less efficient in mitigating the experimental colitis compared to subcutaneous drug solution (PLGA: 7.88 +/- 0.83; P-4135F: 7.48 +/- 0.42; subcutaneous: 5.27 +/- 0.68 U/mg) but superior to drug solution given by oral route (oral: 8.75 +/- 1.34; untreated colitis control: 9.95 +/- 0.92, all U/mg tissue). Tacrolimus solution groups (oral/subcutaneous) exhibited increased levels of adverse effects, whereas both NP groups demonstrated their potential to reduce nephrotoxicity. Both strategies showed similar mitigating effects while nephrotoxic adverse effects were slightly less expressed with pH-sensitive NP.