Egyptian fruit bats are increasingly used as model animals in neuroscience research. Our aim was to characterize suitable injectable anaesthesia for this species, possibly replacing inhalant anaesthesia, thus minimizing occupational health hazards. Eight bats were randomly assigned by a crossover design for subcutaneously administered combinations of medetomidine-midazolam with: saline (MM-Sal), ketamine (MM-Ket), fentanyl (MM-Fen), morphine (MM-Mor), or butorphanol (MM-But). The anaesthetic depth and vital signs were monitored at baseline and every 10 min until bats recovered. If after 180 min the bats did not recover, atipamezole was administered. Mean induction times were 7-11.5 min with all combinations. Twitching during induction was common. All combinations produced anaesthesia, with significantly decreased heart rate (from 400 to 200 bpm) and respiratory rate (from 120-140 to 36-65 rpm). Arrhythmia and irregular breathing patterns occurred. MM-Fen, MM-Mor, and MM-But depressed respiration significantly more than MM-Sal. Time to first movement with MM-Ket and MM-But lasted significantly longer than with MM-Sal. Recovery time was significantly shorter in the MM-Sal (88 min) in comparison to all other treatments, and it was significantly longer in the MM-But (159 min), with atipamezole administered to four of the eight bats. In conclusion, all five anaesthetic protocols are suitable for Egyptian fruit bats; MM-Ket produces long anaesthesia and minimal respiratory depression, but cannot be antagonized completely. MM-Fen, MM-Mor, and MM-But depress respiration, but are known to produce good analgesia, and can be fully antagonized. Administration of atipamezole following the use of MM-But in Egyptian fruit bats is recommended.