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Lower gastrointestinal perforation is rare and challenging to diagnose timeously in the acute abdomen. However, no study has examined the frequency and associated factors of diagnostic errors related to lower gastrointestinal perforation. This large-scale multicenter retrospective study investigated the frequency of diagnostic errors and identified the associated factors. This study retrospectively analyzed data on patient factors, symptoms, situational factors, and physician factors across nine institutions between January 1, 2015 and December 31, 2019. Timely diagnosis was defined as diagnosis at the first visit to a computed tomography (CT)-capable facility or referral to an appropriate medical institution immediately following the first visit to a non-CT-capable facility; cases not meeting this definition were defined as diagnostic errors that resulted in delayed diagnosis. Of the 439 cases of lower gastrointestinal perforation identified, delayed diagnosis occurred in 138 cases (31.4%). Multivariate logistic regression analysis showed a significant association between examination by a non-generalist and delayed diagnosis. Other factors, such as presence of fever, absence of abdominal tenderness, and unavailability of urgent radiology reports, tended to be associated with delayed diagnosis. The initial misdiagnoses mainly comprised gastroenteritis, constipation, and small bowel obstruction. In conclusion, diagnostic errors occurred in about one-third of lower gastrointestinal perforation cases.