OBJECTIVES We assessed the functional significance of side branches after stent implantation in main vessels using fractional flow reserve (FFR). BACKGROUND Little is known about the functional significance of side branches after stent implantation in main vessels in coronary bifurcation lesions. METHODS Between May 2007 and January 2011, 230 side branches in 230 patients after stent implantation in main vessels were assessed by FFR and were consecutively enrolled. RESULTS Mean FFR at side branch was 0.87짹0.10, with only 41 (17.8%) side branches being functionally significant after stent implantation in main vessel. Among 67 side branches with >50% stenosis, 19 (28.4%) had FFR���0.80 and among 163 side branches with ���50% stenosis, 22 (13.5%) had FFR���0.80 after stent implantation in main vessels. Using receiver-operating characteristic curve, the optimal cutoff value of diameter stenosis of side branch was 54.9% and area under the curve was 0.64 (95% CI 0.58-0.71, p<0.001) with a 41.5% sensitivity, an 83.1% specificity, a 34.7% positive predictive value, an 86.3% negative predictive value and a 75.7% accuracy. Multivariate binary logistic regression analysis identified diameter stenosis (odds ratio [OR] 1.04, 95% CI 1.02-1.06, p=0.001) and reference vessel diameter (OR 0.28, 95% CI 0.10-0.77, p=0.014) of side branch before stent implantation as independent predictors of the side branches with FFR ���0.80 after stent implantation. CONCLUSIONS Most side branch lesions do not have functional significance after stent implantation in the main vessel and quantitative coronary angiography is unreliable in assessing the functional severity of these lesions.