An improved method of treating lower urinary dysfunctional epithelium (LUDE) or a disease, condition, or syndrome associated with LUDE, including interstitial cystitis, comprises the step of administering orally a pharmaceutically effective quantity of heparin to a patient in need of treatment for LUDE or a disease, condition, or syndrome associated with LUDE in order to treat LUDE or a disease, condition, or syndrome associated with LUDE. The heparin can be administered together with a quantity of a penetration enhancer that is sufficient to result in a tissue concentration of heparin that is sufficient to treat LUDE or a disease, condition, or syndrome associated with LUDE. A suitable penetration enhancer is sodium N-[8-(2- hydroxybenzoyl)amino]caprylate. The method can further comprise the administration of at least one additional pharmaceutical composition to treat LUDE or a disease, condition, or syndrome associated with LUDE The invention further includes a pharmaceutical composition comprising: (1) a quantity of heparin that is pharmaceutically sufficient for the treatment of LUDE or a disease, condition, or syndrome associated with LUDE; and (b) at least one filler, excipient, or carrier; wherein the pharmaceutical composition is formulated for the treatment of LUDE or a disease, condition, or syndrome associated with LUDE.