The epithalamus of zebrafish presents the best-studied case of directional asymmetry in the vertebrate brain. Epithalamic asymmetries are coupled to visceral asymmetry and include left-sided migration of a single midline structure (the parapineal organ) and asymmetric differentiation of paired bilateral nuclei (habenulae). The mechanisms underlying the establishment of epithalamic asymmetry involve the interplay between anti-symmetry and laterality signals to guide asymmetric parapineal migration. This event triggers the amplification of habenular asymmetries and the subsequent organisation of lateralised circuits in the interpeduncular nucleus. This review will summarise our current understanding on these processes and propose a sequential modular organisation of the events controlling the development of asymmetry along the parapineal-habenular-interpeduncular axis.