Compositions comprising a source of alkaline phosphatase that prevent or reduce toxic influx of lipopolysaccharide (LPS) through mucosal layers of a mamalian body cavity and methods of using these compositions for those purposes are disclosed. Such a source of alkaline phosphatase, preferably in a medical food such as infant milk formula, is eaten, drunk or otherwise administered for prophylaxis or treatment of LPS-mediated or LPS-exacerbated disease