Purpose: The aim of this pilot study was to evaluate subjective and objective findings on short-term post-operative discomfort in patients receiving flapless implant surgery compared to traditional open flap surgery. Materials and Methods: A two-centre, prospective survey study was conducted, using a customized questionnaire. Between December 2010 and January 2012, 20 patients were consecutively included. Eleven received conventional open-flap surgery and nine received flapless surgery. Inflammatory signs, analgesic consumption and sleeping difficulties were evaluated up to seven days postoperatively. A clinical examination was made one week postoperatively. Results: Significantly less experienced swelling was noted 24 hours after flapless surgery compared to open flap surgery for patients receiving four implants or more, and at three days postoperatively for patients receiving single implants. No difference concerning sleeping difficulties, pain or analgesic consumption was found. Clinical examination one week postoperatively showed no differences in wound gaps, redness of the mucosa, or presence of pus between the groups. Conclusions: In conclusion, flapless surgery seems to have a limited effect on postoperative comfort and short-term post-operative signs of soft tissue healing compared to open flap surgery. There is a need for larger randomized trials for evaluating differences in postoperative discomfort between the two surgical techniques.