Making most alien species humanity encounters in sci-fi appear humanoid and very similar-looking to humans makes for incredibly easy casting. There’s no need for costume fittings or hours-long makeup sessions — unless the actor is portraying a Ferengi from Star Trek. This made it exceptionally easy for Doctor Who showrunners to keep Gallifreyans looking identically human, reducing the necessary amount of makeup during production.
However, unlike their outward appearance, Gallifreyans sport some notable internal differences compared to regular homo sapiens, starting with the most notable one — the two hearts. The first instance that the Doctor is confirmed as having two hearts is in the episode Spearhead from Space, the first story of Jon Pertwee’s Third Doctor. In the episode, one of the characters, Doctor Henderson, discovers that the Doctor’s blood supply is different and that he has two hearts.
This was later more dramatically encountered in 1996’s Doctor Who: The Movie, in which Sylvester McCoy’s Seventh Doctor gets shot by members of a street gang. Unconscious, he’s ushered into Walker General Hospital, where the medical personnel removes the bullets, but the Doctor’s two hearts confuse the medical team. Believing that he’s fibrillating (experiencing quivering or irregular heartbeat) and that the X-Ray is showing two hearts due to double exposure, they call in Dr. Grace Holloway to help stabilize the Doctor.
Not knowing what she’s dealing with, Grace attempts to move the microscopic probe during the operation and accidentally damages the unfamiliar circulatory system, mortally wounding the Doctor, who then dies, conscious on the operating table just moments before. His body is later wheeled into the morgue, where he regenerates into Paul McGann’s Eighth Doctor, and Grace later becomes his first companion. But this isn’t the first time Gallifreyan physiology caused confusion and awe in companions.
The companion of David Tennant’s Tenth Doctor, Martha Jones, examined the Doctor in Smith and Jones after he was admitted to a hospital for a made-up circumstance, only to discover that he has two hearts. The hearts were connected via a binary vascular system, which allowed them to operate in unison and compensate in case one of the hearts was damaged or had stopped working, which happened quite a few times in the New Who series.
Naturally, the binary vascular system has to be complemented by a unique respiratory system, or in this case, a respiratory bypass system, which allowed Gallifreyans to go without breathing significantly longer than most humans could. It also allows them to survive inhospitable surroundings filled with toxic fumes. The Doctor even survived several strangulation attempts thanks to the respiratory bypass system.
However, as with regular humans, the circulatory and respiratory systems are interconnected, and when the Doctor’s second heart was extracted, he lost control of his respiratory bypass system, which left him vulnerable to being strangled. This didn’t happen in the series but in the novel The Adventuress of Henrietta Street, so its canonicity is questionable.
The next big physiological difference between Time Lords and humans is that they’re much more resilient against radiation. As seen in the Smith and Jones episode, Gallifreyans are minimally affected by Rontgen radiation (X-Ray), and their children are regularly given radioactive toys in the nurseries. In Smith and Jones, the Doctor safely absorbed a 500% larger dose of X-Ray,
This amount of X-Ray would be fatal to a normal human, transformed it into a form harmless to humans — Martha Jones at that moment — and expelled it from his body. Other types of radiation may be fatal, but Gallifreyans can generally handle much higher doses than regular humans. That isn’t to say that Gallifreyans aren’t susceptible to radiation; they just have a significantly higher tolerance to radiation.
In fact, Gallifreyans are generally much tougher and more resilient than regular humans, and a typical Gallifreyan would be physically superior to a human who’s at the peak of physical performance. They can survive falls that would otherwise shatter human bones, as seen in The End of Time, when the Tenth Doctor survived a fall from a considerable height and was able to stand and walk afterward.
This increase in bone density and physical toughness was never addressed in the show, but it could be credited to the fact that Gallifrey was nearly two times larger than Earth, which also means two times stronger gravity, which could count for an evolutionary advantage of Gallifreyans to have stronger bones and a stronger circulatory system. Again, however, this is purely fandom speculation, as it was never canonically addressed in the series. The stronger circulatory system would also mean better temperature regulation, and Gallifreyans are known to survive extreme cold, extreme heat, and even the vacuum of space — albeit for only six minutes.
Their nervous system is also considerably more complex, and Gallifreyans can have up to three brainstems and separable brain hemispheres that allow them to multitask more easily. Additionally, their brains have an extra lobe that’s entirely dedicated to bodily functions, freeing the rest of their cerebrum for intellectual endeavors. However, most of these differences aren’t visible, and you couldn’t tell a Gallifreyan apart from a regular human — except if you looked them in the eyes.
Human eyes are equipped with light-sensitive cells which transfer visual signals to the brain, which does all the visual processing. Gallifreyans’ retinae, on the other hand, contain neural cells, which allows them to think on their own. Despite that being the only noticeable difference, it’s really hard to notice said differences, as Gallifreyans also have hair and eye color nearly identical to humans. However, there are always exceptions to those rules, as seen in the Destiny of the Daleks, when Romana reincarnated into a form with metallic-looking blue skin.
Matt Smith’s Eleventh Doctor stated that humans “look Time Lord” so it’s highly unlikely for a regular human to recognize a Gallifreyan based on their outward appearance. It would be borderline impossible unless they happened to have a pair of Sonic Sunglasses with X-Ray capabilities at their disposal.