Unlike CT, MRI uses no ionizing radiation. Rather, it uses a powerful magnetic field to align the nuclear magnetization of (usually) hydrogen atoms in water in the body. Radio frequency (RF) fields are used to systematically alter the alignment of this magnetization. This causes the hydrogen nuclei to produce a rotating magnetic field detectable by the scanner. This signal can be manipulated by additional magnetic fields to build up enough information to construct an image of the body.:36

Magnetic resonance imaging is a relatively new technology. The first MR image was published in 1973 and the first cross-sectional image of a living mouse was published in January 1974. The first studies performed on humans were published in 1977. By comparison, the first human X-ray image was taken in 1895.

Magnetic resonance imaging is a development of nuclear magnetic resonance. Originally, the technique was referred to as nuclear magnetic resonance imaging (NMRI). However, because the word nuclear was associated in the public mind with ionizing radiation exposure, it is generally now referred to simply as MRI. Scientists still use the term NMRI when discussing non-medical devices operating on the same principles. The term magnetic resonance tomography (MRT) is also sometimes used.

The body is largely composed of water molecules. Each water molecule has two hydrogen nuclei or protons. When a person goes inside the powerful magnetic field of the scanner, the magnetic moments of some of these protons changes, and aligns with the direction of the field.

In an MRI machine a radio frequency transmitter is briefly turned on, producing an electromagnetic field. The photons of this field have just the right energy, known as the resonance frequency, to flip the spin of the aligned protons in the body. As the intensity and duration of application of the field increase, more aligned spins are affected. After the field is turned off, the protons decay to the original spin-down state and the difference in energy between the two states is released as a photon. It is these photons that produce the electromagnetic signal that the scanner detects. The frequency the protons resonate at depends on the strength of the magnetic field. As a result of conservation of energy, this also dictates the frequency of the released photons. The photons released when the field is removed have an energy — and therefore a frequency — due to the amount of energy the protons absorbed while the field was active.

It is this relationship between field-strength and frequency that allows the use of nuclear magnetic resonance for imaging. Additional magnetic fields are applied during the scan to make the magnetic field strength depend on the position within the patient, in turn making the frequency of the released photons dependent on position in a predictable manner. Position information can then be recovered from the resulting signal by the use of a Fourier transform. These fields are created by passing electric currents through specially-wound solenoids, known as gradient coils. Since these coils are within the bore of the scanner, there are large forces between them and the main field coils, producing most of the noise that is heard during operation. Without efforts to dampen this noise, it can approach 130 decibels (dB) with strong fields (see also the subsection on acoustic noise).

An image can be constructed because the protons in different tissues return to their equilibrium state at different rates, which is a difference that can be detected. By changing the parameters on the scanner, this effect is used to create contrast between different types of body tissue or between other properties, as in fMRI and diffusion MRI.

Contrast agents may be injected intravenously to enhance the appearance of blood vessels, tumors or inflammation. Contrast agents may also be directly injected into a joint in the case of arthrograms, MRI images of joints. Unlike CT, MRI uses no ionizing radiation and is generally a very safe procedure. Nonetheless the strong magnetic fields and radio pulses can affect metal implants, including cochlear implants and cardiac pacemakers. In the case of cardiac pacemakers, the results can sometimes be lethal, so patients with such implants are generally not eligible for MRI.

MRI is used to image every part of the body, and is particularly useful for tissues with many hydrogen nuclei and little density contrast, such as the brain, muscle, connective tissue and most tumors.

In clinical practice, MRI is used to distinguish pathologic tissue (such as a brain tumor) from normal tissue. One advantage of an MRI scan is that it is believed to be harmless to the patient. It uses strong magnetic fields and non-ionizing radiation in the radio frequency range, unlike CT scans and traditional X-rays, which both use ionizing radiation.