Background: Trauma patients sustaining abdominal trauma exhibit high risk of organ failure and/or sepsis aggravating morbidity and mortality during the post-traumatic course. The present study re-evaluates L- and I-FABPs (small fatty acid binding proteins) as early bio-markers for abdominal injury (AI) in a large cohort of patients and analyzes their potential as indicators of specific organ failure and their association with sepsis and/or mortality in the post-traumatic course. Methods: This prospective study included 134 multiply traumatized patients (ISS >= 16). Fifty- nine had AI (abbreviated AI Scale, AIS(Abd) >= 3) and 75 had no AI (noAI). Twenty healthy volunteers served as controls. Plasma I- and L-FABP levels were measured at the admittance to the emergency room (d0) and up to 10 days daily (d1-d10) using ELISA. Sepsis, organ failure, multiple organ failure (MOF) and mortality were assessed. Results: Median L- and I- FABP in the AI-group [258 (IQR=71-500) ng/mL and 328 (IQR=148-640) pg/mL, respectively] were higher compared to noAI-group [30 (IQR = 18-50) ng/mL and 60 (IQR = 40-202) pg/mL, p>0.05] on d0. Sensitivity and specificity to detect AI were 80% and 75% for L- FABP, 78% and 62% for I- FABP. Both FABPs decline with the post-traumatic course to control levels. On d0 and d1, FABPs correlate with the Sepsis-related Organ Failure Assessment (SOFA) score of the following day (d0:rho: 0.33, rho:0.46, d1:rho:0.48, rho:0.35). No other correlations were found. Eight percent of all patients developed sepsis, 18% pneumonia, 4% urinary tract infection, 3% acute kidney failure and one MOF. FABPs correlated neither with Simplifed Acute Physiology Score (SAPS)-II nor to sepsis. All patients with acute kidney failure demonstrated enhanced L-FAPB levels before the increase of serum creatinine levels. Conclusions: Our results confirm the potential of L- and I- FABP to indicate abdominal injuries initially after trauma. Except L- FABP as indicator of acute kidney failure both FABPs have to be further evaluated as predictors for other organ failures, sepsis and/or mortality.