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Recent reports have demonstrated that the new commercially available immobilized-type chiral stationary phases (CSPs) containing amylose tris(3-chloro-5-methylphenylcarbamate) (ACMPC) as a selector exhibit not only an exceptionally high enantioselectivity in high-performance liquid chromatography (HPLC) but they are also applicable to a wide range of chiral analytes. Herein, we report the results obtained in the HPLC analysis of omeprazole and its impurities B and E on the ACMPC-based Chiralpak IG-3 CSP (CSP) under polar organic conditions. A systematic evaluation of the retention characteristics of the selected benzimidazole chiral probes was carried out by changing the composition of the mobile phase and the column temperature. It is worth emphasizing that the high affinity of both enantiomers of all analytes recorded in pure methanol mode dramatically decreased incorporating small volumes of either basic or acid additives in the mobile phase. Unspecified sites of the IG-3 CSP presumably involved in strong and non-stereoselective H-bonding contacts with chiral analytes are assumed responsible for the unproductive retention process.