Breathing system filters are recommended for use during general anaesthesia. Manufacturers of gas sampling equipment recommend that gas is sampled from the 'machine side' of these filters, thereby avoiding contamination of the sampling line and waterlogging in the case of heat and moisture exchangers. The aim of this study was to investigate differences between the measured end-tidal carbon dioxide values at either side of the filter. Fifteen adults were studied during mechanical ventilation and 15 during spontaneous ventilation under general anaesthesia. End-tidal carbon dioxide values were significantly lower at the machine side of the filter in both groups (p = 0.00001). The measurement error induced by the inclusion of the breathing system filter was significantly greater in the spontaneously breathing group (p = 0.0004).