Abstract: Introduction: Posterior uveitis (PU) and retinal vasculitis (RV) are the main morbidity factor in Behcet’s Disease (BD). They usually progress toward severe loss of vision or blindness. They need aggressive treatment with cytotoxic drugs. Azathioprine was demonstrated, in a double blind control study, to be effective in Behcet’s Disease. The aim of this study was to evaluate the efficacy of Azathioprine in ocular lesions of BD, and to compare its efficacy with Pulse Cyclophosphamide (PCP). Materials and Methods: We used the same protocol that we have used for other cytotoxic drugs in the treatment of ocular lesions of BD. Twenty-nine patients were selected randomly. They received 2-mg/kg azathioprine daily. They also received 0.5-mg/kg/daily of prednisolone. Upon the control of inflammation prednisolone was gradually tapered. A Disease Activity Index (DAI) was calculated for anterior uveitis (AU), the PU, and the RV. Visual acuity (VA) was calculated with a Snellen chart. A Total Adjusted Disease Activity Index (TADAI) was calculated for each patient comprising the inflammatory indexes of both eyes and the visual acuity. A confidence interval (CI) was calculated for each percentage. All DAI before and after the treatment were compared by the Student paired t test. Results: The mean follow up time was 7.2 months (minimum 3 months, maximum 14 months). The entry data were as follow. The mean DAI was 3.1 for AU, 2.4 for PU, and 2.4 for RV. The mean VA was 3.8, and the mean TADAI was 38.3. After the treatment the mean DAI for AU improved to 1.4 (p<0.004) and for PU to 1 (p<0.001). It remained the same for RV (no improvement). The mean VA improved to 4.9 (p<0.005), and the mean TADAI to 29.2 (p<0.001). AU improved in 76% (CI=11.3), PU in 75% (CI=12), RV in 48% (CI=14.8), and VA in 55% (CI=12.8) of the eyes. TADAI improved in 69% (CI=16.8) of patients. Discussion: For comparison, 115 patients were selected from our cohort of 359 patients under PCP, to have approximately the same mean follow up time (7.6 months). AU improved in 64% (CI=6.2), PU in 62% (CI=6.6), RV in 57% (CI=7.3), and VA in 45% (CI=6.5) of the eyes. TADAI improved in 70% (CI=8.4) of patients. Looking at the percentages and their CI, there was no statistically significant difference between azathioprine and PCP. However the mean DAI for RV didn’t change with azathioprine while it significantly improved with PCP. Conclusion: Azathioprine is best indicated for patients with PU alone. It is better to avoid it for patients with RV.