To evaluate the changes in aqueous vascular endothelial growth factor (VEGF) and pigment epithelium-derived factor (PEDF) following intravitreal bevacizumab injections for choroidal neovascularization (CNV) secondary to age-related macular degeneration or pathologic myopia. Aqueous samples were obtained at the time of injection from 51 eyes of 51 patients who underwent three monthly intravitreal bevacizumab (Avastin) injections at baseline, 1, and 2 months. Concentrations of VEGF and PEDF in the aqueous were evaluated using enzyme-linked immunosorbent assay and compared. For the 34 eyes with age-related macular degeneration CNV, the mean +/- standard deviation aqueous VEGF level reduced from 102.6 pg/mL +/- 90.6 pg/mL at baseline to 18.3 pg/mL +/- 22.5 pg/mL at 2 months (P < 0.001), whereas the mean PEDF level increased from 11.2 ng/mL +/- 10.4 ng/mL at baseline to 38.7 ng/mL +/- 47.9 ng/mL at 2 months (P = 0.001). For the 17 eyes with myopic CNV, the mean +/- standard deviation aqueous VEGF level reduced from 20.1 pg/mL +/- 28.9 pg/mL at baseline to 3.8 pg/mL +/- 5.3 pg/mL at 2 months (P = 0.016), whereas the mean PEDF level increased from 20.0 ng/mL +/- 16.3 ng/mL at baseline to 126.0 ng/mL +/- 152.0 ng/mL at 2 months (P = 0.016). Intravitreal bevacizumab injections resulted in reduced aqueous VEGF and increased PEDF levels in patients with CNV secondary to age-related macular degeneration or pathologic myopia. These changes may be favorable for the inhibition of CNV angiogenesis.