Intraoperative microvascular complications in autologous breast reconstruction significantly increase the risk of post-operative complications. No study has identified which specific intraoperative complications contribute to partial or total flap loss. A retrospective chart review of microsurgical breast reconstructions by five surgeons between 2009-2020 analyzed operative variables and patient outcomes, with complications determined from the operative report. Flap loss rates were compared between cases with and without intraoperative complications. Statistical analysis was performed using Fischer exact and t-tests for discrete and continuous variables, respectively. Intraoperative complications were analyzed for 1465 autologous breast flaps performed in 916 patients. Early partial flap loss was predicted by arterial anastomosis revision (2.90% vs 0.44%, p=.03) and alternate venous outflow (14.29% vs 0.41%, p=.002), with no association with intraoperative thrombosis, venous revision, or difficult recipient or flap dissection. In comparison, early total flap loss was predicted by intraoperative arterial revision (5.80% vs 0.51%, p=.001), venous revision (5.45% vs 0.57%, p=.007), intraoperative thrombosis (12.12% vs 0.49%, p<.001), and difficult flap dissection (2.91% vs 0.59%, p=.04). Difficult flap dissection was the only intraoperative variable associated with late partial flap loss (6.80% vs 1.69%, p=.004). Late total flap loss only occurred in 6/1465 flaps, the sole association being difficult recipient vessel dissection (2.78% vs 0.29%, p=.03). Post-operative arterial and venous compromise occurred in 1.10% (13/1187) and 2.53% (30/1187) of cases with no intraoperative complications, respectively, compared to 3.2% (9/278, p=0.02) and 6.12% (17/278, p=0.002) in cases with an intraoperative complication. Alternate venous outflow predicts early partial flap loss, while intraoperative thrombosis, and arterial and venous revision predict early total loss. Difficult flap dissection was associated with early total and late partial flap loss, while difficult recipient vessel dissection was associated with late total flap loss.