The objective of this study was to assess patency of the internal jugular vein following modified radical or selective neck dissection and microvascular flap reconstruction by power Doppler ultrasound and its impact on free flap survival. In 23 patients who underwent selective or modified radical neck dissection and microvascular flap reconstruction the patency of the internal jugular vein was examined by power Doppler ultrasound on the first post-operative day and after follow-up of at least four months. On the first post-operative day in one patient partial thrombosis was found, while in the other 22 patients the internal jugular vein was normal patent. During follow-up in 17 (74 per cent) patients a normal patent internal jugular vein was found, while partial and complete thrombosis were found in three (13 per cent) patients each. On the first post-operative day 22 of the 23 (96 per cent) free flap veins were visualized. There was no free flap loss during follow-up. Power Doppler ultrasound is a valuable diagnostic technique for determination of internal jugular vein patency and may be useful as screening method or in case of clinical suspicion of thrombosis to determine internal jugular vein patency. Late internal jugular vein thrombosis may probably not effect free flap survival due to neovascularization.