The influence of gut microbiota on the toxicity and metabolism of hydrazine has been investigated in germ-free and 'conventional' Sprague Dawley rats using 1H NMR based metabonomic analysis of urine and plasma. Toxicity was more severe in germ-free rats compared with conventional rats for equivalent exposures indicating that bacterial presence altered the nature or extent of response to hydrazine and that the toxic response can vary markedly in the absence of a functional microbiome.