Abstract Brain-derived neurotrophic factor (BDNF) has been reported to rescue neuroretinal cells under different toxic conditions. These cells include not only those expressing BDNF receptors (TrkB) but also those not expressing TrkB including photoreceptors. The purpose of this study was to determine the retinal sites at which BDNF and TrkB isoforms are expressed after different durations of continuous light exposure, and to compare these sites with those of TUNEL-positive cells in the same retina. Sprague–Dawley rats were exposed to continuous light for different durations. The expressions of BDNF and TrkB isoforms, TrkB-FL and TrkB-T1, were determined by Western blot analysis, real-time PCR, immunohistochemistry, and in situ hybridization before and after the light exposure. The number of TUNEL-positive cells reached a maximum at 48 to 72 h after light exposure. The degree of up-regulation of the TrkB-T1 gene was significantly higher than that in normal control eyes at 24 h by real-time PCR. Immunohistochemistry showed that TrkB-FL-positive cells were detected in all retinal layers except the outer nuclear layer (ONL), photoreceptor cells, and retinal pigment epithelium (RPE). The number of TrkB-FL-positive cells in the IPL was transiently decreased at 6 h, and was increased on the processes of the Mueller cells in the ONL after 48 h. TrkB-T1 was expressed in the INL, OPL, and RPE, and was up-regulated on the soma of Mueller cells after 24 h. In situ hybridization showed that the expression of the TrkB-FL gene was up-regulated in the INL after 48 h when the number of TUNEL-positive cells was at its peak. The TrkB-T1 gene was up-regulated before or just prior to the appearance of TUNEL-positive cells. These results suggest that BDNF transduces the signals using appropriate receptor isoforms that are expressed temporally and spatially differentially on Mueller cells during light-induced retinal degeneration.