The study analyzed 135 women with laparoscopically confirmed intestinal endometriosis and examined how the size and location of the lesion affected the severity of symptoms. Large rectal lesions (Enzian C3 classification) were associated with more severe pain during defecation, presence of blood in the stool, and abdominal pain compared with smaller lesions (Enzian C1–C2). Blood in the stool was observed only in patients with involvement of the rectal area (Enzian C). Patients with lesions in other parts of the intestine (Enzian FI) had a higher risk of bloating compared to patients with only rectal involvement. Combined lesions in the rectal area and other intestinal parts were associated with more severe presence of blood in the stool and pain during defecation. The size of lesions in other intestinal parts did not have a significant effect on the severity of symptoms, although the analysis was probably underpowered. The results suggest that the location and size of intestinal lesions are important factors in predicting the severity of symptoms in women with intestinal endometriosis.