The membranous and soluble isoenzymes of alkaline phosphatase (AP-ase) were isolated from the duodenal mucosal cells in control and cysteamine-treated rats. Both the cytosolic and membranous isoenzymes of the AP-ase were drastically inhibited by a single subcutaneous injection of cysteamine-HCl, a potent duodenal ulcerogen. However, cysteamine did not change the isoenzyme distribution between the two compartments of the duodenal mucosal cells. Membranous isoenzyme of duodenal AP-ase in control rats was separated by concanavalin A (Con A) affinity chromatography into three fractions: unbound (65%), weakly bound (11 %) and strongly bound (24%). The strongly bound fraction disappeared completely from duodenal mucosal cells of cysteamine-treated rats before any visible signs of ulcer formation. Since the strongly bound fraction of AP-ase contains high mannose-type sugar chains, we concluded that the ulcerogen affected the initial mannosylation (or glypiation) of membranous AP-ase which took place in the rough endoplasmic reticulum of the mucosal cells. In control rats, the Con A fractions of the membranous AP-ase were separated by gel filtration as tetramers of Mr 420 and 340 kD and dimers of Mr 185-200 kD. In cysteamine-treated rats, neither the strongly bound tetramers of 340 kD nor dimers of 185 kD were found by gel filtration. However, cysteamine did not change the total tetramer:dimer ratio. Judging by the decrease of Vmax values at the pH optimum, the different molecular forms of the AP-ase are selectively sensitive to cysteamine inhibition. The kinetic data show that the type of the tissue-specific inhibition by cysteamine is different for dimeric and tetrameric forms of the membranous AP-ase. It is of an ‘uncompetitive’ type for a tetrameric form and of a ‘non-competitive’ type for dimeric forms.