For children under the age of three, taking the temperature in the bottom is the most accurate method.
Taking a rectal measurement is not irritating, unless of course you take your child's temperature too often. Remember that you should only take a temperature reading if your child seems ill and/or feverish. It's not advised to take your child's temperature every day for reassurance or to aid bowel movement.
Choose a digital thermometer with a fine tip for your child. It's practical and gives a signal after about sixty seconds to let you know the reading is finished.