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The objective of this prospective randomised clinical study was to determine the differences in the tracheal, oesophageal and rectal temperature in spontaneously breathing or mechanically ventilated dogs. A total of thirty dogs were allocated to the SPO-group breathing spontaneously (n = 15) or the MEC-group ventilated mechanically (n = 15). Anaesthesia was established using a medetomidine-butorphanol-propofol-isoflurane combination. The tracheal (T-Tra), oesophageal (T-Oes), rectal (T-Rec), inspired gas (T-Gas), room (T-Room) temperatures, respiratory frequency (fR), heart rate (HR), mean arterial pressure (MAP) and end-tidal carbon dioxide concentration (ETCO2) were measured after connecting to a re-breathing system (baseline) and subsequently in 10-minute intervals for 60 minutes. The data were analysed using ANOVA and Steel-Dwass tests (P < 0.05). In the SPO-group, the T-Tra, was significantly lower at T30, T40, T50, T60, the T-Oes and T-Rec at T40, T50, T60, compared to the baseline. In the MEC-group, the T-Tra and T-Oes was significantly lower at T30, T40, T50, T60, the T-Rec at T40, T50, T60, compared to the baseline. In the SPO-group, the fR was significantly lower for all the times and the ETCO2 higher at T10, T20, T30, T40, T50 compared to the MEC-group. No other differences were detected. During anaesthesia, there is a comparable decrease in body temperatures, regardless of whether the dogs are breathing spontaneously or ventilated mechanically.