Bimorpholine and bipiperidine are efficient organocatalysts. Stereoselectivity of reactions catalysed by bimorpholine and bipiperidine strongly depend on their protonation - only the protonated form of the catalyst leads to stereoselective reactions. In this study the conformations of these compounds, as well as some reaction intermediates, are investigated computationally. Significant changes in the conformations are observed when the compounds are protonated, caused by intramolecular hydrogen bonding. (C) 2009 Elsevier B.V. All rights reserved.