This study was performed to assess the immediate and long-term patency of stent-associated side branches (SB) according to the types of stent. A total of 314 patients with 332 lesions (CrossFlex stent 86, NIR 100, GFX 146) had 365 SB (>1 mm) covered by coronary stents. Side branch occlusion (SBO) occurred in 7.7% of CrossFlex stent, in 10.5% of NIR stent and in 8.8% of GFX stent (P = NS). SBO primarily occurred in SB with ostial disease, and the presence of SB ostial disease was the only independent predictors of SBO after stenting (OR 22.1, 95% CI 9.47-51.49, P < 0.001). At 6 months follow-up, 11 of 31 SBO regained the patency, but the remaining SB had persistent SBO. Delayed SBO occurred in 8 SB, being associated with the presence of SB ostial disease and in-stent restenosis. In conclusions, SBO was not associated with the types of stent design, but with the SB lesion morphology.