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Neural substrates, including brain areas, differential gene expression and neuroendocrine basis, of migration are known. However, very little is known about structural changes in the brain that underlie the development and cessation of migration in long-distance avian migrants. Towards this, we investigated neuromorphological changes in the higher-order associative areas in male redheaded bunting (Emberiza bruniceps), which is a Palaearctic–Indian night migrant with wintering grounds in India. Photosensitive birds (8L:16D; SD) were exposed to stimulatory long days (16L:8D; LD), with controls retained on non-stimulatory short days. LD birds depicted shifts to, and sustained night-time activity as recorded by actograms. LD birds demonstrated increased body mass, fat deposition and testicular volume in keeping with the migratory phenotype. When LD birds had exhibited 10.0 ± 2.4 cycles of Zugunruhe (intense nighttime activity in captives, akin to night migratory flight in the wild), bird brains were fixed by transcardial perfusion, and changes in the neuronal morphometry of pallial, sub-pallial and hypothalamic brain regions studied using rapid Golgi technique with modifications, as used and validated in our laboratory. There were significant differences in both area and perimeter of soma in the visual hyperpallium apicale implicated in migratory orientation and the neuroendocrine control region for timing of migration, the mediobasal hypothalamus. We attribute these neuromorphometric changes in the soma area and perimeter to the photostimulated changes associated with the development of migration and reproductive phenotypes in redheaded buntings. It is suggested that changes in the neuronal plasticity in brain control regions parallel photoperiod-induced physiological responses. [ABSTRACT FROM AUTHOR]