Objective Peritoneal biopsies are considered useful for gaining a better understanding of the pathophysiology of the peritoneum during experimental peritoneal dialysis (PD). Different peritoneal tissue samples (i.e., abdominal wall, liver, diaphragm, intestine, and omentum) may be used, but there can be artifacts due to peritoneal tissue processing. Aim To investigate differences in peritoneal membranes from different parts of the peritoneum, and also 2 different fixatives, in experimental PD and a peritonitis model in rats. Methods Peritoneal tissues from the anterior abdominal wall, liver, omentum, and intestine were taken from each of 3 groups of animals: sham, experimental PD, and peritonitis model. Tissue samples were immediately fixed with 4% formaldehyde and routinely processed for histological examination. Two parietal peritoneal tissue samples according to longitudinal and horizontal sections of anterior wall inner abdominal muscle were also taken. All samples were immediately fixed with 4% formaldehyde and B5 fixative (B5), and then routinely processed for histological examination. Results In all groups, histopathological findings were more commonly seen in the abdominal wall samples. There were no changes observed in peritoneal membranes other than those of anterior abdominal wall samples from both sham and PD model rats. However, there was a significant difference between anterior and posterior facets of liver in the peritonitis model. Furthermore, the antimesenteric site of intestinal peritoneum was less affected than the mesenteric site. There were no significant histopathological differences between B5 and 4% formaldehyde fixation ( p > 0.05). Conclusion Our results suggest that peritoneum obtained from the anterior abdominal wall is the most affected area and therefore the most suitable site to investigate peritoneal changes in the experimental rat PD model. There were no significant differences between fixation with 4% formaldehyde and B5 solution. Abdominal wall samples should be of the same direction of inner abdominal muscle, that is, horizontal sectioning should be used for measurements of the submesothelial area.