In the electronics industry, wafer cleaning is usually performed by means of hot ammoniacal or acidic hydrogen peroxide solutions, which remove organic surface films by oxidative breakdown and dissolution to expose the substrate surface for concurrent and/or subsequent decontamination reactions. It is difficult to establish the optimum renewal cycle of the cleaning solutions to avoid economic as well as pollution problems. The present work deals with the application of ion chromatography to the determination of anionic as well as cationic impurities in hydrogen peroxide and ammonia, which are extensively used in wafer cleaning technology. As these two reagents cannot be injected directly into the separator column, methods are suggested for the pretreatment of the samples. Hydrogen peroxide was subjected to UV photolysis for about 30 min in an UV digestor at 85 ± 5°C. Though ammonia could also be treated in the same manner, simply heating it at 85 ± 5°C for 45 min in a dust-free cell, to expel most of the ammonia as gas, was found to be satisfactory. The samples were then analysed by ion chromatography and were found to contain chloride, phosphate, sulphate, copper, zinc, iron and manganese as impurities in variable amounts, when analysed at different stages of the wafer cleaning operation (20–1000 μg/l).