A novel analytical approach based on pyrolysis-gas chromatography coupled with mass spectrometry of carbohydrates with in situ silylation using hexamethyldisilazane is presented in this work for the first time. A micro reaction sampler was used to simultaneously achieve the pyrolyis reaction and facilitate the derivatization of pyrolysis products, by enabling the materials to react with the derivatizing agent in a sealed capsule at high temperature and pressure for long periods of time. This drastically increased the complete silylation of the pyrolysis products and the chromatographic resolution, resulting in less complex pyrograms and increased sensitivity toward the most stable compounds. Different results were obtained for glucose and cellulose in terms of predominant pyrolytic pathways. The formation of anhydrosugars was the preferential pyrolytic reaction for glucose, while the formation of cyclopentenones and small molecules was predominant for the pyrolysis of cellulose. Steric hindrance effects of polysaccharide chains on the efficiency of the derivatizing agent were hypothesized in order to explain the different results. A good reproducibility was found, with relative standard deviations not greater than 10%. Semiquantitative calculations showed that the partial silylation of anhydrosugars was almost completely overcome after 10 min of reactive pyrolysis. This work discloses a powerful and potentially widely applicable analytical method for the investigations of organic materials under controlled pyrolytic conditions, with the advantage of increasing the effectiveness of in situ derivatization.