Retinal axons undergo an age-related reorganization at the junction of the chiasm and the optic tract. We have investigated the effects of removal of chondroitin sulphate on this order change in mouse embryos aged embryonic day 14, when most axons are growing in the optic tract. Enzymatic removal of chondroitin sulphate but not keratan sulphate in brain slice preparations of the retinofugal pathway abolished the accumulation of phalloidin-positive growth cones in the subpial region of the optic tract. The loss of chronotopicity was further demonstrated by anterograde filling of single retinal axons, which showed a dispersion of growth cones from subpial to the whole depth of the tract. The enzyme treatment neither produced detectable changes in growth cone morphology and growth dynamic of retinal neurites nor affected the radial glial processes in the tract, indicating a specific effect of removal of chondroitin sulphate from the pathway to the axon order in the tract. Although chondroitin sulphate was also found at the midline of the chiasm, growth cone distribution across the depth of fibre layer at the midline was not affected by the enzyme treatment. These results suggest a mechanism in which retinal axons undergo changes in response to chondroitin sulphate at the chiasm–tract junction, but not at the midline, that produce a chronotopic fibre rearrangement in the mouse retinofugal pathway.