The successful separation of 2- and 3-methyl-substituted positional isomers of butanol, butyl acetate, and butanoic acid and its ethyl ester, is reported. These compounds are of interest in the study of wine flavour, however the separation of the 2- and 3-methyl isomers may present problems, and more so in the presence of the wine matrix components, when single capillary column gas chromatography (GC) is used. The strategy to achieve separation was based on the use of shape-selective cyclodextrin derivative (CDD) capillary columns (commonly referred to as chiral columns). These columns provide simultaneous resolution of the enantiomeric pairs of the 2-methyl isomers, and at the same time the ability to separate the 3-methyl isomer from the 2-methyl is achieved in all but the case of the ( S)-2- and 3-methylbutanol. The advantages of using shape-selective columns to perform this study is demonstrated, with coupling of two CDD columns giving improved separations of these compounds. Although these compounds are relatively volatile, cryogenic modulated comprehensive two-dimensional GC was shown to provide good pulsed peak profiles with chiral separation in the first dimension when a thicker film trapping column segment was employed. The components of interest were well separated from other wine matrix components.