An alternative procedure of orthogonalization involving a metric matrix of the linear vector space formed by the columns of LCAO matrix is introduced. It is proved that this procedure is fully equivalent the original Lowdin's scheme. Also, a few modifications involving a two-step orthogonalization scheme are outlined and briefly discussed. Numerical results of test calculations of atomic charges for several representative molecules seem to fully validate the newly proposed methodology. (C) 2011 Elsevier B.V. All rights reserved.