Breathing system filters are in common use during paediatric anaesthesia. Expired gas sampling from the patient side of these filters may contaminate and saturate the sampling line, while sampling from the machine side may cause underestimation of end-tidal carbon dioxide (PECO 2). The aim of this investigation was to elucidate the degree of underestimation of PECO 2 induced by sampling from the machine side of a breathing system filter. Ten spontaneously breathing children and ten children receiving mechanical ventilation under general anaesthesia were studied. PECO 2 was higher at the patient side of the filter in both ventilated and spontaneously breathing groups (P<0.002 for each). The bias in measuring at the machine side of the filter was significantly greater in the spontaneously breathing children as compared with the mechanically ventilated children (-1.8 vs -0.7 kPa; P<0.004).