Diverse procedures have been reported for the separation and analysis by HPLC of the two major glycoalkaloids present in potatoes, alpha-chaconine and alpha-solanine. To further improve the usefulness of the HPLC method, studies were carried out on the influence of several salient parameters on the analysis of the two potato glycoalkaloids. Effects on retention (elution, separation) times of the (a) composition and pH of the mobile phase (acetonitrile and phosphate buffer), (b) concentration of the phosphate buffer, (c) capacity values of column packing of four commercial HPLC amino columns, (d) column temperature were studied. Except for pH, all of the variables significantly influenced the retention times. The results make it possible to select analysis conditions that produce well-separated as well as symmetrical peaks of the two glycoalkaloids. This improved HPLC method (limit of detection of approximately 150 ng) was evaluated with extracts from the cortex of one whole potato variety (May Queen) grown in Japan and the freeze-dried peel and flesh from the following eight cultivars grown in the United States: Atlantic, Dark Red Norland, Ranger Russet, Red Lasoda, Russet Burbank, Russet Norkota, Shepody, and Snowden. In addition, the same samples were analyzed by GC-MS for the presence of two water-soluble nortropane alkaloids, calystegine A(3) and calystegine B(2), reported to be potent glycosidase inhibitors. The following ranges for the eight varieties of total glycoalkaloid and calystegine levels were observed: dry flesh, 5-592 and 6-316 mg/kg; dry peel, 84-2226 and 218-2581 mg/kg; dry whole potatoes, 40-883 and 34-326 mg/kg; wet flesh, 1-148 and 1-68 mg/kg; wet peel, 12-429 and 35-467 mg/kg; wet whole potatoes, 7-187 and 5-68 mg/kg. The possible significance of the results to plant and food sciences is discussed.