The veterinarian should be consulted as to whether or not the animal should be fasted, and for what time period. There is great variation among species: regurgitation rarely occurs in rats and fasting may cause life threatening hypoglycemia; whereas, prolonged fasting in ruminants will reduce bloat and the risk of regurgitation and pulmonary aspiration. Bathing some animals may be necessary to remove excess dirt and hair and is best done the day before the scheduled surgery.

On the day of surgery, the surgeon and assistants should wash their hands. It is advisable to wear clean, non-sterile gloves at all times the animal is being handled. It is preferable to wear a clean (not sterile) gown over the scrub suit while preparing the animal.

In a preparation area physically separate from the location where the surgery will be performed, the animal should be anesthetized and intubated. In general, intubation is recommended for all warm-blooded vertebrates, since the endotracheal tube minimizes the potential for aspiration of stomach contents. In addition, the endotracheal tube allows for positive pressure ventilation should emergency resuscitation be required.

Hair over the surgical site should be clipped and the loose hair picked up by a vacuum system. Hair removal should be done carefully to avoid causing small skin abrasions. Hair should be removed over a liberal area to anticipate any surgical emergency and minimize wound contamination from adjacent areas. Because anesthetized rodents experience excessive heat loss, a much smaller area should be clipped - only the hair directly over the surgical site. After clipping the hair, the skin should be washed with an antiseptic surgical scrub, containing soap, to remove remaining hair and dirt.

The surgical area is cleansed two more times with antiseptic scrub and the scrub solution rinsed away with alcohol. A final antiseptic solution (devoid of soap) is sprayed or swabbed along the proposed incision and is not rinsed. The site is covered with clean gauze sponges or cotton, saturated with the antiseptic solution devoid of soap, and the animal transported to the surgical area. The protective gowns (now dirty and covered in hair) should be removed in the animal preparation area. The surgeon and assistants should now put on caps and masks.

When animals are placed directly on metal surgery tables, body heat is lost, therefore insulating materials or warming devices should be placed between the table and the animal. Circulating warm water heating pads or warm water bottles should be used, since electric heating pads are likely to burn. When heat lamps are used, avoid placing the animal in the direct beam. If possible, reflect the heat lamp off of a metal surface and place the animal in the reflected beam.

The surgical site should be draped to isolate the surgical field from the surrounding areas. Drapes are positioned and fixed with towel clamps and should not be dragged across unsterile areas onto the surgical field. Even with rodents and other small animals, the surgical incision site should be draped.