The expression of mRNA for brain-derived neurotrophic factor (BDNF) is regulated by early visual experience. In this study, we sought to determine whether other neurotrophic factor mRNAs are similarly regulated. We reared pigmented rats from birth to postnatal day 21 in a normal light cycle, constant light (LR) or constant darkness (DR). In the retina, superior colliculus (SC), primary visual cortex (V1), hippocampus (HIPP) and cerebellum (CBL), using a ribonuclease protection assay (RPA), we examined expression of the mRNAs for nerve growth factor (NGF), BDNF, NT3, NT4, ciliary neurotrophic factor (CNTF) and glial cell line-derived neurotrophic factor (GDNF). LR or DR alter the expression of the mRNAs for NGF, BDNF and NT3 and CNTF within the visual system. LR also upregulated BDNF mRNA expression within the cerebellum. In all of the structures examined, NT4 mRNA expression was unaltered by LR or DR and GDNF mRNA was undetectable. Notably, the same rearing condition could induce changes of opposite sign in the mRNA for a single factor in different structures or for different factors in the same structure. Thus, during developmental stages when sensory experience and neuroelectric activity are important in the shaping of visual circuitry, vision regulates the expression of multiple neurotrophic factor mRNAs and each mRNA has a unique profile with respect to the locus and sign of activity-induced changes.