Abstract: Background– Controversy exists whether histology/immunohistochemistry (IHC) or clonality testing is more appropriate to diagnose IBD and SCL in cats, and whether the diagnostic method affects the ultrasonographic differentiation between both entities. Objectives– To compare utrasonographic measurements between IBD and SCL diagnosed either by H/IHC or clonality testing and to evaluate effects of standardized treatment in a subset of cats. < br>Animals– 16 client-owned cats. Methods– Duodenal, jejunal and ileal total wall, mucosa, muscularis propria and submucosa thicknesses were quantified and ratios (muscularis/submucosa, muscularis/total wall thickness) calculated. All cats underwent standardized full-thickness duodenal, jejunal and ileal biopsies. Samples for clonality testing were frozen; treatment was based on H/IHC. Intestinal segments were grouped by diagnosis either based on H/IHC or clonality testing and ultrasonographic measurements were compared between IBD/SCL using a linear mixed model. Ultrasonographic measurements were repeated in 7 cats (5 IBD,2 SCL) after 12 and 24 weeks of treatment. Differences were compared using a mixed model. Results– Based on each of the two methods (H/IHC and clonality testing), 11 cats had IBD and 5 cats had SCL. Discordant results between diagnostic methods were found in 6/16 (38%) cats. Ultrasonographic differences were not found between IBD and SCL independent of the chosen diagnostic method. During treatment, muscularis/total wall thickness ratio decreased by 0.053 every 12 weeks of the study (p=0.0254) in IBD cats. Conclusions and clinical importance– Regardless of the diagnostic method, ultrasonographic findings did not differ between IBD and SCL. Change over time in IBD cats was minimal and thus of questionable clinical benefit.