The efficacy of a novel carbohydrate extraction procedure was investigated with methylation analysis and alditol acetate method by Gas Chromatography-Mass Spectrometry. A published extraction procedure for β-glucans was compared to one developed in house. Both procedures gave a dominant glucose peak in the Gas chromatogram indicative of successful β-glucan isolation. Further linkage studies showed four linkage positions for β-glucans isolated with the published method; terminal, 1,3-linkage, 1,6-linkage and 1,3,6-linkage, while β-glucans isolated using the new method showed six linkage positions; terminal, 1,3-linkage, 1,6-linkage, 1,4-linkage, 1,2,3-linkage and 1,3,6-linkage. Diminishing β-glucan linkage peaks in the chromatogram for the published method indicated structure degradation. The results for mannan isolated with 50 mM base gave mannose as a dominant component compared to mannan isolated with 50 mM acid. Base extracted mannan also indicated a good yield of mannan in hyphal form of Candida albicans. This has not been reported with other published isolation methods.