A balloon catheter for treating a condition of a vessel near a bifurcation comprises a shaft including a proximal and distal end, and a side surface, at least one guide wire lumen extending longitudinally, a distal port extending from the guide wire lumen through the distal end, a side port extending transversely from the guide wire lumen through the side surface, and a balloon mounted on the shaft. The balloon comprises a first end sealed to the shaft proximally of the side port, a second end sealed to the shaft distally of the side port and an aperture aligned with the side port. A portion of the balloon surrounding the aperture is sealed to the shaft around the side port. The balloon may be guided to the bifurcation on a first and a second guide wires pre-positioned in main and in side branch vessel, respectively.