The purpose of the paper is designation of the changes in the structure of cellulose after the methane fermentation process of Miscanthus and Sorghum harvested during the growing season and afterwards. The percentage and structure of cellulose before and after fermentation were studied. Investigations into changes of the cellulose structure were conducted by the SEC, FT-IR and XRD methods. The average percentage of cellulose after the growing season for Miscanthus varieties was higher and for Sorghum varieties was lower. As a result of the fermentation, the percentage of cellulose for both investigated species harvested in two growth seasons was lower. The degree of polymerisation for the plants harvested after the growing season was lower for the most feedstock. As a result of the fermentation process, the degree of polymerization increased for each of the investigated feedstock. However, crystallinity of cellulose remained at the same level for Miscanthus and decreased for Sorghum. It was shown that changes were different in the cellulose structure of the compared species.