<p>Exercise-induced gastrointestinal syndrome (EIGS) involves disruption of intestinal barrier integrity during strenuous physical exercise. Although EIGS has been extensively studied in running and cycling, gastrointestinal responses to rowing remain poorly characterized. This study evaluated biomarkers of intestinal epithelial damage and gut permeability following a maximal 6000-m rowing ergometer test. Twenty-one elite male rowers from the Polish National Team completed a maximal 6000-m rowing ergometer trial. Blood samples were collected before exercise, after exercise, and after 1&#xa0;h of recovery. Serum concentrations of intestinal fatty acid-binding protein (I-FABP), claudin-3 (CLDN-3), lipopolysaccharide (LPS), and lipopolysaccharide-binding protein (LBP) were measured using enzyme-linked immunosorbent assays. CLDN-3, LPS, and LBP changed significantly over time, with the largest alterations observed during recovery. Post hoc analyses indicated recovery-related increases in CLDN-3, LPS, and LBP. Significant correlations were found between LPS and CLDN-3 (<i>r</i> = 0.431), LPS and I-FABP (<i>r</i> = 0.381), and CLDN-3 and I-FABP (<i>r</i> = 0.313). A maximal 6000-m rowing effort was associated with transient alterations in biomarkers of intestinal barrier integrity and endotoxin-related responses, with the most pronounced changes observed during early recovery. These findings suggest that prolonged high-intensity rowing may contribute to exercise-induced gastrointestinal perturbations in elite athletes.</p><p>Trial registration: NCT06890741 (registered retrospectively).</p>