A pharmaceutical composition comprising therapeutically effective amount of rifaximin or pharmaceutically acceptable salt or enantiomer or polymorph thereof, pharmaceutically acceptable excipient(s) and release controlling agent(s). Pharmaceutical composition of rifaximin comprising: at least two entities wherein one entity is an immediate release or fast release and the other is controlled release. The pharmaceutical composition in the form of multilayer tablet comprising, at least one layer comprising, therapeutically effective amount of rifaximin or pharmaceutically acceptable salt or enantiomer or polymorph thereof, pharmaceutically acceptable excipient(s); said layer providing controlled release rifaximin; and at least one layer which provides increased residence time of the dosage form in the gastrointestinal tract. The pharmaceutical formulation comprising rifaximin having an in vitro dissolution profile, wherein about 70% of rifaximin is released in about 24 hours. The composition comprising therapeutically effective amount of rifaximin or pharmaceutically acceptable salt(s) or enantiomer(s) or polymorph(s) thereof, one or more release controlling agent(s) and pharmaceutically acceptable excipient(s) causing pathogenic eradication.