Background There is an increasing demand for successful free tissue transfer, with postoperative monitoring of flaps a key to early salvage. Monitoring methods have ranged from clinical techniques to invasive options, of which two are particularly applicable to buried flaps (Cook-Swartz Doppler probe and microdialysis). The evidence for these options has been represented largely in separate cohort studies, with no single study comparing these three techniques. We aim to perform this comparison in a single cohort of patients. Methods A prospective, consecutive cohort study comparing clinical monitoring, microdialysis and the implantable Doppler probe was undertaken. In 20 patients receiving 22 flaps, 21 flaps were monitored with microdialysis, 18 flaps with clinical observation, and 21 flaps with the Cook-Swartz Implantable Doppler probe. Exclusion was based on applicability and availability intra-operatively. Efficacy was assessed through sensitivity, specificity, positive, and negative predictive values. Results Nineteen of 22 flaps had no suspected anastomotic problems; 3 of 22 flaps were explored for anastomotic problems, with two salvaged and one lost. The implantable Doppler and microdialysis were found to detect flap statistically earlier than clinical assessment, with microdialysis better at detecting flap compromise: 100 specificity (confidence interval 31-100 ) when compared to the implantable probe and clinical assessment (67 : 13-98 and 33 : 2-87 , respectively). Conclusions Each of the Cook-Swartz Doppler probe, microdialysis and clinical assessment was found suitable for monitoring in free tissue transfer. The implantable Doppler and microdialysis offer the potential for earlier detection of flap compromise. ? 2014 Wiley Periodicals, Inc. Microsurgery 35:262-271, 2015. ? 2014 Wiley Periodicals, Inc.