An improved HPIC method has been developed and validated for ammonium analysis using a high efficiency analytical column (smaller particle size, 5.5 um and narrower inner diameter, 3 mm). Compared to the widely used Health Canada HPIC method, the improved method is faster (25 min per sample instead of 50 min per sample), simpler (two mobile phases of water and MSA needed instead of three mobile phases as in HC method) and 10 times more sensitive with the limit of detection at 0.004 ug/mL and limit of quantification at 0.013 ug/mL. Both linear and quadratic calibration methods were evaluated with correlation coefficients larger than 0.99. Another significant improvement of the method is that it can completely separate ammonium peak from interfering peaks of organic amines and therefore, better accuracy of the results can be achieved. The method can be applied to ammonia analysis in a wide range of tobacco sample matrices including cigarette smoke samples, cigarette filler, tobacco-related extracts and smokeless tobacco samples. Examples of the applications will be presented using different reference tobacco samples such as Kentucky reference cigarettes KY 3R4F and KY 1R5F, CORESTA Monitoring CM 6 and CORESTA reference for smokeless tobacco CRP-3, as well as commercial cigarette smoke samples.