Effects of brain-derived neurotrophic factor (BDNF) on cell migration from the ventricular zone to the cortical plate (CP) in developing mouse cerebral cortex were examined. BDNF (700 ng) was injected into the brain ventricle of 13- or 14-day-old embryos (E13 or E14) after the intraperitoneal administration of 5-bromodeoxyuridine (BrdU) to pregnant mice. BDNF injection at E13 increased the number of BrdU-positive cells migrated into the CP until E15, and caused them to become localized in much deeper layers (V-VI) than expected (IV-V, as in the vehicle-treated mice) by postnatal day 1. However, when the injections were made at E14, BrdU-positive cells predominantly migrated to layers II/III irrespective of BDNF administration. These results demonstrate that BDNF affects particular progenitors at limited stages, and suggest the presence of a Reelin-independent mechanism(s) to regulate cell migration.