The headspaces above faecal and urine samples provided by six pigs have been analysed using selected ion flow tube mass spectrometry (SIFT/MS). The concentrations of ammonia, nitric oxide, nitrogen dioxide, acetone, methanol, ethanol, dimethyl sulphide (DMS) and low molecular weight carboxylic acids in the headspace volume were measured down to the parts per billion (ppb) levels. The differences in the relative concentrations of these compounds between faeces and urine, the implications of these differences and the advantages of using SIFT/MS in such diagnostic and physiological monitoring work are discussed.