BACKGROUND Ischemia/reperfusion (IR) injury of the intestine is a major problem in abdominal pathological condition and is associated with a high morbidity and mortality. The purpose of the study is to determine whether the L-carnitine can prevent the harmful effects of small intestinal IR injury in rats. METHODS Thirty Sprague-Dawley rats were randomly divided into three groups. Sham operated group (S), for shamoperated, the IR group for rats submitted to 45-minute of intestinal ischemia and 2-hour reperfusion, and IR+L group for those IR group treated with L-carnitine before reperfusion. All the rats were given EmGFP labelled E. coli DH5α through gavage 2-hour before the operative procedure. Afterwards the bacterial translocation (BT) from mesenteric lymph nodes (MLN), liver, spleen, lung and portal vein blood were detected. And the colony forming units/g (CFU/g) were counted. The TNF-α, IL-1β, IL-6, and IL-10 in serum were measured by ELISA. The morphometric study was measured by Chius classification. RESULTS The levels of BT were higher in the IR group than IR+L group (P < 0.05). The E. coli DH5α was hardly detected in the S group. The IR+L rats had enhancement of IL-10 and suppressed production of serum TNF-α, IL-1β and IL-6, compared to IR group rats (P < 0.05). The degree of pathological impairment in small intestine was lighter in IR+L than IR group (P < 0.05). CONCLUSIONS The L-carnitine pretreatment has a positive effect on reducing levels of BT, on inhibiting secretion of proinflammatory cytokines, and on lessening intestinal mucosa injury during small intestinal IR injury. BACKGROUND L-carnitine; Ischemia/reperfusion injury; Intestine.