The present prospective cohort study evaluates the effect of three-dimensional (3-D) endoscopy on outcome in transphenoidal endoscopic surgery of pituitary adenomas compared to conventional two-dimensional (2-D) endoscopy. Prospective data was collected from patients undergoing endoscopic surgery for pituitary adenomas before and after the introduction of 3-D endoscopy. Patients, grouped by having 2-D or 3-D endoscopic surgery, were compared in regard to procedure time, intraoperative blood loss, complications, hospital stay, grade of resection and quality of life (QoL). Twenty-six patients having surgery with 2-D endoscopy were compared with 29 patients having surgery with 3-D endoscope. Only primary procedures were included. There were no significant differences in baseline characteristics between the two groups. No statistically significant differences in outcome were noted with 3-D endoscopy. Procedure time, complication rate, hospital stay, rate of gross total resection and post-operative QoL were unaffected by surgical technique though there were non-significant increases in new pituitary insufficiency with 3-D endoscopy and diabetes insipidus with 2-D endoscopy. This prospective cohort study fails to show obvious outcome advantages with 3-D endoscopy in pituitary surgery using basic parameters including post-operative QoL. To our knowledge this is the first prospective study published on the matter, thus corroborating results from previous retrospective studies with similar results on 3-D neuroendoscopy and 3-D endoscopy in general. The main advantage of increased depth perception is more likely found in more complex extended transphenoidal skull base procedure.