The chromatin structure determines gene expression and thereby regulates developmental processes in the plant. The molecular mechanisms regulating the induction and release of seed dormancy are still largely unknown and the underlying changes in chromatin organization have hardly been analyzed. Most chromatin studies in plants have been performed on vegetative tissues and have focused on seedlings. The composition of seeds hampers molecular analyses and requires adaptation of the methods that are used for other tissues. Here, we give an overview of the current methods that are used to study different aspects of chromatin organization in seeds. Cytogenetic methods, like fluorescence in situ hybridization and immunolocalization, are used to study chromatin at the microscopic level. Changes in DNA methylation and histone modifications can be studied with molecular methods, like bisulfite sequencing, immunoblotting, and chromatin immunoprecipitation.