Chronic lymphocytic enteritis (CLE) is a frequent disease in common marmosets. However, no diagnostic test for early detection of CLE is available. Mast cells have an important role in gastrointestinal disease. The purpose of this study was to measure fecal concentrations of N-methylhistamine (NMH), a breakdown product of histamine metabolism, in common marmosets. A previously established NMH gas chromatography-mass spectrometry assay for canine feces and urine was used, and partial validation was performed. The reference intervals (n = 30) established for fecal NMH concentrations in common marmoset were 118.2 ng/g or less for a single fecal sample, 121.7 ng/g or less for the 3-d mean, and less than or equal to 167.5 ng/g for the 3-d maximum. Considerable day-to-day variation was observed in fecal NMH concentrations; the mean %CV was 42.2% (minimum, 7.1%; maximum, 141.4%). Fecal NMH concentrations were measured in 14 marmosets for which necropsy reports were available; 7 of the 8 marmosets with CLE and the 1 animal with lymphoma and ulcerative enteritis had increased fecal NMH concentrations. Increased fecal NMH concentrations may serve as a potential marker for CLE; however, further studies exploring the role of mast cells in marmosets with CLE are needed.