The retention behavior of thirteen alkylated guanines on normal-phase silica gel and amino columns and on reversed-phase ODS and phenyl columns was studied. The larger the alkyl substituent at the same position of guanine the weaker was the retention in the normal-phase chromatographic system and the greater the retention during reversed-phase chromatography. O6-Derivatives possess the lowest polarity in each set of isomers. An amino column was found to be of highest efficiency in terms of separation of the set of ethylguanine isomers and of benzylguanines studied. A phenyl column provided the best resolution of methylated guanines.