Background: Deep sclerectomy and similar procedures including a deroofing of Schlemm’s canal are meeting with increasing interest owing to the limited risk profile of non-perforating glaucoma surgery. The aim of our study was to investigate how often the outer wall of Schlemm’s canal or parts of the trabecular meshwork were incorporated in the excised tissue on deep scleral flap dissection by an experienced glaucoma surgeon.  Methods: The excised deep scleral flap was prepared for light microscopy after performing deep sclerectomy in 7 children and 22 adult patients suffering from glaucoma. Meridional serial sections were checked for the presence of fragments of trabecular beams and collector channels and parts of the endothelial wall of Schlemm’s canal. Morphology was compared with the intraoperative appearance of the operated tissue. Results: In 15 patients (52%) the deep scleral flap contained at least some tissue from the outer wall of Schlemm’s canal; in 5 of these 15 patients noticeable remnants of the juxtacanalicular trabecular meshwork were also found, although only in one patient was this obvious during surgery. In 14 patients (48%) no evidence of the deroofing of Schlemm’s canal was found within the excised deep scleral flap, although intraoperatively the dissection seemed to have been too superficial in only 5 patients. Conclusion: Even when performed by an experienced glaucoma surgeon, deep sclerectomy produces biopsy material of remarkable morphological variability that does not always correspond to the intraoperative appearance of the site of operation. More than in conventional trabeculectomy this variability may be of importance for the outcome of surgery.