The purpose of this study was to design novel colon specific drug delivery system containing flurbiprofen (FLB) microsponges. Microsponges containing FLB and Eudragit RS 100 were prepared by quasi-emulsion solvent diffusion method. Additionally, FLB was entrapped into a commercial Microsponge® 5640 system using entrapment method. Afterwards, the effects of drug:polymer ratio, inner phase solvent amount, stirring time and speed and stirrer type on the physical characteristics of microsponges were investigated. The thermal behaviour, surface morphology, particle size and pore structure of microsponges were examined. The colon specific formulations were prepared by compression coating and also pore plugging of microsponges with pectin:hydroxypropylmethyl cellulose (HPMC) mixture followed by tabletting. In vitro dissolution studies were done on all formulations and the results were kinetically and statistically evaluated. The microsponges were spherical in shape, between 30.7 and 94.5 μm in diameter and showed high porosity values (61–72%). The pore shapes of microsponges prepared by quasi-emulsion solvent diffusion method and entrapment method were found as spherical and cylindrical holes, respectively. Mechanically strong tablets prepared for colon specific drug delivery were obtained owing to the plastic deformation of sponge-like structure of microsponges. In vitro studies exhibited that compression coated colon specific tablet formulations started to release the drug at the 8th hour corresponding to the proximal colon arrival time due to the addition of enzyme, following a modified release pattern while the drug release from the colon specific formulations prepared by pore plugging the microsponges showed an increase at the 8th hour which was the time point that the enzyme addition made. This study presents a new approach based on microsponges for colon specific drug delivery.