The integrity of the intestinal barrier is crucial for regulating the passage of pathogens and toxins, while facilitating nutrient absorption. The everted gut sac technique, an ex-vivo technique, can be used to study interventions on barrier function. This cost-effective approach utilizes relatively large gut segments to study specific intestinal regions. Typically, intact (non-stripped) intestinal segments are used, but their use may underestimate permeability due to the medial positioning of blood vessels relative to the seromuscular layer and serosa. However, removing these layers risks physical damage, resulting in an overestimation of intestinal permeability. Therefore, we investigated the impact of stripping jejunal segments on permeability to fluorescein isothiocyanate-dextran (FITC, 4kDa) and tetramethylrhodamine isothiocyanate-dextran (TRITC, 40kDa), and on the absorption of glucose, lysine, and methionine in jejunal segments from 80 piglets at 8 d postweaning. Piglets were subjected to either high or low sanitary housing conditions and diets provoking intestinal protein fermentation or not, expected to influence intestinal permeability. Stripping of the seromuscular layer and serosa increased the passage of 4kDa FITC-dextran (stripped vs. non-stripped; 1.1 vs. 0.9 pmol/cm2/min, P < 0.001), glucose (40.0 vs. 19.1 pmol/cm2/min, P < 0.001), lysine (2.5 vs. 2.0 nmol/cm2/min, P < 0.001), and methionine (4.1 vs. 2.7 pmol/cm2/min, P < 0.001). As permeability increased, the differences in methionine passage between stripped and non-stripped intestinal segments also increased (slope = 1.30, P = 0.009). The coefficients of variation were comparable between stripped and non-stripped intestines (over all treatments, stripped vs. non-stripped 38% vs. 40%). Stripping, by isolating mucosal processes without introducing additional variation, is thus recommended for studies on intestinal permeability or absorption.