Purpose: To compare the short-term ocular hypotensive efficacy and side effects of 0.2% brimonidine and 0.5% apraclonidine in patients with elevated intraocular pressure (IOP). Methods: We performed a double-masked, placebo-controlled study to compare the efficacy of the application of 0.2% brimonidine and 0.5% apraclonidine for the effect of IOP, systemic blood pressure and heart rate in 20 newly diagnosed ocular hypertensive patients. Effects on the untreated fellow eye and ocular side effects were also determined. All measurements were performed 1, 2, 4, 6 and 8 h after the instillation of one drop. Results: Brimonidine and apraclonidine significantly reduced IOP from baseline at all observation times. No significant difference was observed between the treatment groups. IOP decreased significantly in the untreated fellow eye in the brimonidine group at 4-, 6- and 8-hour checks and at 6-hour checks in the apraclonidine group when compared with placebo. Blood pressure and heart rate decreased significantly in the brimonidine group compared with placebo. Apraclonidine did not affect blood pressure or heart rate any differently than placebo. The pupil diameter and the interpalpebral fissure width significantly increased in the apraclonidine group, but not in the brimonidine group. There were no significant differences in the overall incidence of foreign body sensation, burning and stinging and dry mouth in the treatment groups. Conclusions: In the short-term, brimonidine was effective in reducing IOP in patients with elevated IOP and was equivalent in efficacy to apraclonidine. On the other hand, a significant change in blood pressure and heart rate was observed with brimonidine; there was no change at all in the apraclonidine group.