Studies on immune cells derived from the human intestine are needed to understand the pathogenesis of gastrointestinal diseases and to develop novel treatment strategies. Isolation techniques to extract these immune cells from intestinal tissue are largely based on murine studies and comparative data on isolation from human intestine is scarce. In this study we evaluated cell yield, viability, and surface-molecule expression on mononuclear leukocytes, comparing three techniques to obtain a single immune cell suspension from human intestine; low concentrations of either the enzymes Collagenase D or Liberase TL, and enzyme-free mechanical dissociation with the Medimachine. Both enzymatic isolation techniques provided a higher cell yield than mechanical dissociation. Expression of surface molecules remained intact after Collagenase D treatment, while Liberase TL digestion resulted in a strong decrease in the expression of the CD4 receptor. Taken together, Collagenase D digestion provides the highest yield of mononuclear cells while keeping surface molecule expression intact.