Lateralisation occurs when the left and right sides of the brain are specialized or dominant for different cognitive functions. In chickens (Gallus gallus domesticus) and other birds, the orientation of the embryo in the egg late in development causes asymmetrical illumination of the eyes, which in turn triggers the development of some lateralised behaviours. To investigate molecular mechanisms underlying brain lateralisation in birds—and how it is affected by differential illumination of the eyes—brains were harvested from embryonic-day-18 (E18) and four-day-old (P4) chickens incubated either in the light or dark. Brains were divided into left and right halves and dissected into telencephalon and remaining brain mass (excluding cerebellum). The data showed that changes in gene expression in E18 chickens reflected known light-induced anatomical asymmetries in the visual system. In P4 chickens the greatest differences in gene expression were observed in the telencephalon. Differential light stimulation of the eyes therefore results in differential gene expression in the brain that may underlie the development of anatomical and functional lateralisation. The differentially expressed genes and transcription factors identified here provide a mechanism to localize lateralisation-relevant structural changes in brain anatomy in greater detail than before.