Intraoperative assessment of coronary artery bypass grafts (CABG) anastomotic quality can be performed using transit-time flowmetry (TTF). The aim of this study was to compare on- versus off-pump coronary graft TTF and early postoperative outcomes. Between January 2009 and January 2010, 521 distal graft flows were assessed using TTF measurements in 253 consecutive patients undergoing primary isolated CABG surgery. Data were analyzed using multilevel models accounting for clustering among surgeons and grafts performed in the same patient. Mean age was 66 ± 10 years and 22% were female (n = 55) with 34% diabetics (n = 86) and 40% preoperative myocardial infarction (MI) (n = 101). The surgeries were performed off-pump in 67% (n = 170) with sequential vein grafts in 57% (n = 144) of patients. Off-pump patients had higher pre-operative left ventricular ejection fractions (LVEF), fewer urgent surgeries, fewer distal anastomoses, and fewer sequential vein grafts (all p<0.001). Intra-operative coronary graft TTF measurements were lower in sequential vein grafts performed off-pump versus on-pump. More patients in the on-pump group needed milrinone or dobutamine 24-48h postoperatively (p = 0.005). Independent predictors of lower TTF included female gender and off-pump surgery, whereas predictors of better TTF were preoperative MI, larger coronary diameter at the site of the distal anastomosis, and sequential vein grafting. Lower intra-operative TTF measurements were found in sequential vein grafts in off-pump CABG. However, off-pump patients experienced similar short-term outcomes compared to on-pump patients.