Modern molecular cytogenetics allows observation of various aspects of nuclear genome organisation at the level of chromosome or in the interphase nucleus. Cytomolecular analysis has enabled us to investigate fundamental aspects of Brachypodium genome structure, such as arrangement of chromosome territories during interphase, meiotic chromosome behaviour and localisation of the proteins involved in key meiotic events. Moreover, we have begun investigating epigenetic regulation, focusing particularly on nucleolar dominance. The studies were conducted by using fluorescence in situ hybridisation with chromosome specific BAC clones, immunofluorescent localisation in situ of the proteins known to play crucial roles at early meiosis, such as synaptonemal complex proteins and immunostaining with specific antibodies raised against particular epigenetic modifications. Brachypodium distachyon as a model organism is now very much on its way to become the ‘Arabidopsis thaliana of the Poaceae’. The challenge now is to determine to what extent these models are representative of other groups of plants. This study should significantly further our understanding of small nuclear genome organisation and could contribute to general understanding of grass genome structure and dynamics. The authors acknowledge financial support from Polish Ministry of Science and Higher Education (grant N N303 570738). AB, NB and EB acknowledge scholarships from the UPGOW project co-financed by the European Social Fund.