Background: Three-dimensional (3D)-imaging modalities for pre-operative mapping of perforators in DIEP and ms-TRAM flap surgery are well established. While zonal perfusion of such flaps has been extensively studied pre-, intra- and post-operatively, the role of objective perfusion assessment for decision making between different possible perforator configurations has not been investigated yet. In this study, a combined lased Doppler spectrophotometry (CLDS) system was applied intra-operatively to support the surgeon's decision-making process. Methods: In this prospective study, 25 consecutive unilateral abdominal flaps were included. Computed tomographic angiography (CTA) was performed prior to surgery. By CLDS the post-capillary oxygen saturation, relative haemoglobin content and relative bloodflow were determined at different time points and in four standardised zones in dependence of different possible perforator/pedicle vessel configurations (with selective clamping of different perforators and/or the superficial inferior epigastric vein). Results were correlated with clinical findings and late results were evaluated after 6-16 months. Results: Ninety-six percent of the flaps survived. No significant fat necrosis was observed. While there was a high correlation between clinical findings and CLDS results, CLDS was more sensitive in identification of venous congestion of DIEP flaps. The technique helped to identify the dominant perforator(s) in flaps where perfusion patterns were unclear. CLDS influenced intra-operative decision making in five cases (two venous and one arterial in-flap anastomosis and inclusion of additional perforators in two flaps). Conclusion: Intra-operative use of CLDS helps to objectively determine perfusion patterns in abdominal flaps. CLDS might be applicable in 'complex' abdominal flaps (e.g., after previous abdominal surgery or when preoperative CTA does not provide conclusive results) and supports, in these cases, intra-operative decision-making.