The simplest & least intrusive way is to listen to the heartbeat. If it has two beats (one heart), it's a human; if it has four beats (two hearts), it's a Time Lord. Indeed, this is the criterion used by Donna Noble and the Tenth Doctor in "The Doctor's Daughter" to determine what Jenny is. It's also been noted in a few stories that their body temperature is noticeably different. And in "A Good Man Goes to War", Time Lords are shown to have their own form of DNA. "Human Nature" (novel) (later adapted as the TV episodes "Human Nature" and "The Family of Blood"), and the later "Utopia" revealed that it is possible for Time Lords to suppress certain physical elements (such as their second heart) in order to pass as human by use of the Chameleon Arch.