Guinea pigs (GPs) are difficult to anaesthetize successfully, the choices for anaesthesia are limited and physiological parameters are likely to be influenced substantially under anaesthesia. We implanted blood pressure radio-telemetry devices into 16 male GPs and subjected them to anaesthesia with ketamine-xylazine (KX), medetomidine-midazolam-fentanyl (MMF) or isoflurane (Iso, plus atropine premedication) in a randomized order with a 7 day interval between anaesthesias. Each anaesthesia lasted 40min, after which Iso was discontinued, MMF was fully antagonized with atipamezole-flumazenil-naloxone and KX was partially antagonized with atipamezole. Hemodynamics were recorded continuously for at least 240min after induction and the GPs were monitored for respiratory rate, reflex responses and specific observations until regaining of their righting reflex (RR). Blood for glucose testing was taken from the ear at 7.5, 20 and 40min during anaesthesia. Recovery time was short with MMF and Iso but long for KX. MMF induced only a transient blood pressure drop after antagonization, whereas Iso caused a marked hypotension during maintenance and KX led to moderate hypotension after antagonization. MMF and Iso produced tolerable heart rate changes, but KX led to long term post-anaesthetic bradycardia. Hypothermia occurred with all anaesthesias, but the GPs returned to normothermia the fastest under MMF, followed shortly by Iso. KX, however, caused a profound and prolonged hypothermia. The respiration was depressed with all anaesthesias, substantially with MMF (-41%) and KX (-52%) and severe during Iso maintenance (-71%). Blood glucose with MMF and KX increased throughout the anaesthesia, but the values remained within reference values with all anaesthetics. The reflex responses character and strength varied between the anaesthetics. In conclusion, MMF is the anaesthetic of choice and Iso may be used for short, non-painful procedures. We advise against the use of KX in GPs.