Objectives The aim of this study was to evaluate serum haptoglobin as a biomarker to differentiate between small-cell alimentary lymphoma and inflammatory bowel disease in cats. Methods Client-owned domestic cats with and without chronic gastrointestinal signs were enrolled in the study. Serum was collected from each patient and serum haptoglobin levels were measured using ELISA. In cats with gastrointestinal signs, histopathologic evaluation of endoscopic biopsies harvested from the intestinal tract was used to separate them into inflammatory bowel disease and small-cell lymphoma cohorts. Serum haptoglobin levels were statistically analyzed and compared among the three groups: healthy cats; cats with inflammatory bowel disease; and cats with small-cell alimentary lymphoma. Results Sixty-two cats were enrolled in the study, including 20 clinically normal cats, 14 cats with small-cell alimentary lymphoma and 28 cats with inflammatory bowel disease. The mean ± SD serum haptoglobin was 73.2 ± 39.1 mg/dl in normal cats, 115.3 ± 72.8 mg/dl in cats with inflammatory bowel disease and 133.1 ± 86.1 mg/dl in cats with small-cell alimentary lymphoma. Cats with inflammatory bowel disease and lymphoma had significantly higher serum haptoglobin than controls, with P values of 0.0382 and 0.0138, respectively. There was no statistical difference between the inflammatory bowel disease and lymphoma cohorts ( P = 0.4235). For every one unit increase in serum haptoglobin, the odds of gastrointestinal inflammatory disease (inflammatory bowel disease or small-cell alimentary lymphoma) increased by 1.41% ( P = 0.0165). Conclusions and relevance Serum haptoglobin is a useful biomarker for distinguishing between normal cats and those with gastrointestinal inflammatory disease, but it could not significantly differentiate between inflammatory bowel disease and lymphoma. Additional studies may be beneficial in determining the prognostic significance of serum haptoglobin as it may relate to the severity of gastrointestinal inflammation.