CD44 expressed in monocytes and lymphocytes seems to play a crucial role in gastrointestinal inflammation, such as the one occurring in the context of inflammatory bowel diseases. Differentially methylated genes are distinctly expressed across monocyte subpopulations related to the state of Crohn's disease. Hence, the aim of this study was to detect CD44 expression in leukocyte subpopulations in relation to the type of IBD, therapy, and disease duration. Monocyte subpopulations CD14(++)CD16(-), CD14(++)CD16(++), and CD14(++)CD16(+) as well as other leukocytes were analyzed for their CD44 expression using flow cytometry in 46 patients with IBD and 48 healthy controls. Patients with Crohn's disease treated with non-biological therapy (NBT) exhibited a lower percentage of anti-inflammatory CD14(+)CD16(+) monocytes, whereas NBT-treated patients with ulcerative colitis had lower expression of CD44 on CD14(+)CD44(+) lymphocytes in comparison to controls, respectively. Conversely, patients with Crohn's disease treated with biological therapy had a higher percentage of CD44(+) granulocytes but lower expression of CD44 on anti-inflammatory monocytes compared to controls. Median fluorescence intensity (MFI) of CD44 on CD44(+)CD14(+) lymphocytes was higher in ulcerative colitis patients treated with biological therapy compared to NBT. The percentage of classical CD14(+)CD16(-) monocytes was lower in the <9 years of IBD duration subgroup compared with the longer disease duration subgroup. The present study addresses the putative role of differentiation and regulation of leukocytes in tailoring IBD therapeutic regimes.