Strangulating small intestinal disease (SSID) in horses carries a poor prognosis for survival, especially following resection of ischaemic tissue. The margins of a resection are principally based on visual appraisal of the intestine during surgery. We hypothesized that histological evaluation of resected tissue may identify occult changes indicative of prognosis. Small intestinal samples from 18 horses undergoing resection for SSID and 9 horses euthanised for reasons unrelated to gastrointestinal pathology were utilised. Histological appearance was used to generate a ‘total damage score’ (TDS) for the control tissue, grossly normal tissue at oral and aboral extremities (sections OR1 and AB1) of the resected intestine, and oral and aboral extremities of visually abnormal tissue (sections OR2 and AB2) from SSID horses. The relationship between TDS and long-term post-operative survival was investigated. TDS was not different between control tissues and OR1 and AB1 sections. Five surgical cases were alive at follow-up, the longest follow-up time being 2561 days. Based on the median scores for SSID cases versus controls, cut-off values were generated to evaluate post-operative survival versus TDS. Only OR2 TDS was significantly associated with survival, with a higher (worse) score indicating longer survival. More severe tissue insult may expedite rapid progression to surgery, improving post-operative outcomes.