While most of the bilaterian body is symmetrical with respect to the midline, a few functions have evolved to be concentrated on one (left or right) side. Although long thought to be a human-specific characteristic, it is now clear that lateralisation of the brain is an evolutionarily conserved mechanism to add layers of complexity to brain function and enable lateralised behaviour within the population. Here, to shed light on how brain asymmetries arise during vertebrate development and to what extent underlying molecular mechanisms are conserved within different species, zebrafish and chick embryonic epithalamus has been studied. By two-photon laser ablations, cell transplants and high-resolution imaging, we find that the exact timing of regulation by the parapineal – a small left-sided group of cells in the zebrafish epithalamus – is essential for the establishment of overt molecular and anatomical asymmetries described in the the adjacent habenulae. However, whole-mount in situ hybridisation, RT-PCR and qPCR experiments show no apparent asymmetries in gene expression patterns of chick epithalamus. Since no region equivalent to parapineal has yet been discovered in birds, it is likely that the anatomical and functional asymmetries found in the epithalamus of vertebrates such as fish, reptiles and amphibians, result from the emergence of a parapineal or a parapineal-like organ during evolution.