Pyrolysis-gas chromatography (Py-GC) is a powerful tool for the detailed compositional analysis of polymers. A major problem of Py-GC is that polar (bio)polymers yield polar pyrolyzates which are not easily accessible to further GC characterization. In the present work, a newly developed fully automated procedure for thermally assisted hydrolysis and methylation (THM) of biopolymers is described. Drying of the sample, addition of the reagent, incubation and pyrolysis are performed inside the liner of a programmable temperature vaporizer injector. The new system not only allows efficient analysis of large series of samples, but also allows automated optimization of the experimental parameters based on an experimental design approach. The performance of the automated THM-procedure was evaluated by performing THM-GC of a poly(acrylic acid)-poly(maleic anhydride) copolymer (PAA/PMAH) and several polysaccharides. The optimized THM-procedure was applied for the structural characterization and differentiation of several lignins and hydroxypropylmethyl-celluloses. It was also applied to proteins. Here myoglobin and cytochrome c were used as the model compounds. Both conventional GC-mass spectrometry (MS) and comprehensive two-dimensional gas chromatography (GC Γ GC)-time-of-flight (TOF) MS were used for separation and identification of the species formed. The information obtained can aid in structure elucidation of polar biopolymers as well as in providing detailed compositional information which can be used to differentiate structurally similar biopolymers