Prolonged peritoneal dialysis (PD) is responsible for progressive morphological changes such as deterioration of the peritoneal membrane. These changes increase the risk of encapsulating peritoneal sclerosis (EPS). Histological assessments of peritoneal membrane biopsy samples are fundamental for the evaluation of the peritoneal damage caused by PD. For evaluating serial morphological changes induced in the peritoneum by PD, we recommend to perform peritoneal biopsy examinations not only after the cessation of PD but also before performing PD. At the time of PD catheter insertion, the parietal peritoneum (1.5 × 1.5 cm) and rectus abdominal muscle posterior sheath is sampled at a point 3 cm below the PD catheter insertion site. Furthermore, at the time of PD catheter removal, the parietal peritoneum is sampled at a point 3 cm apart from the PD catheter insertion site to avoid artifacts. The peritoneum should be evaluated to detect mesothelial cell denudation, acellular sclerotic changes and thickness of the submesothelial connective tissue, vasculopathy of the post-capillary venules, vascular angiogenesis, and new encapsulating membrane. The method presented herein allows the minimization of surgical invasiveness and artifacts of the specimens and safe performance of peritoneal biopsy examinations. Morphological evaluation of the peritoneum involving an appropriate biopsy strategy, in conjunction with functional markers of deterioration, such as peritoneal permeability or cytokine levels, is a useful approach for examining peritoneal damage and predicting the prognosis of PD patients, especially the onset of EPS.