A mesocyclone is a meso-gamma mesoscale (or storm scale) region of rotation (vortex), typically around 2 to 6 mi (3.2 to 9.7 km) in diameter, most often noticed on radar within thunderstorms. In the Northern Hemisphere, it is usually located in the right rear flank (back edge with respect to direction of movement) of a supercell, or often on the eastern, or leading, flank of a high-precipitation variety of supercell. The area overlaid by a mesocyclone’s circulation may be several miles (km) wide, but substantially larger than any tornado that may develop within it, and it is within mesocyclones that intense tornadoes form.

Mesocyclones are medium-scale vortices of rising and converging air that circulate around a vertical axis. They are most often associated with a local region of low-pressure. Their rotation is (usually) in the same direction as low pressure systems in a given hemisphere: counter-clockwise in the northern, and clockwise in the southern hemisphere, with the only occasional exceptions being the smallest-scale mesocyclones. Mesoanticyclones that rotate in an opposite direction may accompany mesocyclones within a supercell but these tend to be weaker and often more transient than mesocyclones, which can be sustained for tens of minutes or hours, and also cyclically form in succession within a supercell. Mesoanticyclones are relatively common with left-moving supercells that split from parent supercells in certain vertical wind shear regimes.

A mesocyclone is usually a phenomenon that is difficult to observe directly. Visual evidence of rotation – such as curved inflow bands – may suggest the presence of a mesocyclone, but the cylinder of circulating air is often too large to be recognized when viewed from the ground, or may not carry clouds distinct enough from the surrounding calmer air to make the circulating air flow obvious.

Mesocyclones are identified by Doppler weather radar observations as a rotation signature which meets specific criteria for magnitude, vertical depth, and duration. On U.S. NEXRAD radar displays, algorithmically identified mesocyclones, such as by the mesocyclone detection algorithm (MDA), are typically highlighted by a yellow solid circle on the Doppler velocity display; other weather services may have other conventions.^{[citation needed]}

They are of greatest concern when contained within severe thunderstorms, since mesocyclones often occur together with updrafts in supercells, within which tornadoes may form near the interchange with a downdraft.

Mesocyclones are localized, approximately 2 km (1.2 mi) to 10 km (6.2 mi) in diameter within strong thunderstorms. Thunderstorms containing persistent mesocyclones are supercell thunderstorms (although some supercells and even tornadic storms do not produce lightning or thunder and thus are not technically thunderstorms). Doppler weather radar is used to identify mesocyclones. A mesovortex is a similar but typically smaller and weaker rotational feature associated with squall lines.

One of the main ingredients for mesocyclogenesis is the presence of strong changes in wind speed over distance and direction with height, also known as horizontal and vertical wind shear. This shear classically coincides with the presence of a strong trough which may lead to an extratropical cyclone, a type of cyclone that forms through the interactions between cold and warm air, known as baroclinicity. The pressure and temperature gradients between warm and cold air cause these changes in the wind with height and over distance. The resulting sheared wind field is said to have horizontal vorticity, or the local tendency of the flowing fluid (here, air) to rotate, which is a property fundamental to any flow where velocity gradients exist.

The associated vorticity is often incorrectly depicted as a horizontally-rolling vortex that is directly tilted into the vertical by a rising updraft. However, in the majority of cases, the environment is horizontally homogenous with horizontal roll vortexes being absent. Horizontal vorticity can instead be thought as an imaginary paddle wheel that is set spinning by the winds that change with height. These winds move the top and bottom of the wheel at different speeds along the horizontal direction, causing it to twist along its axis. This local tendency for rotation, or twisting, is what the updraft reorients, rather than a literal tube or vortex of rotating air. When an updraft forms in this environment, ascending air parcels encounter faster sheared air across height, which is entrained and turbulently mixed at the edge of the updraft, exchanging horizontal momentum. The rising air at the edge speeds up sideways faster than it's moving inward, forcing inner slower air to then also move faster horizontally. Air parcels then begin to curve as they move towards and overshoot the updraft's center of low pressure, following into a spiral as the process repeats. As the air parcels curve they also rotate about their axis due to the wind shear's twisting motion. This curving, spiraling or rotating motion of the wind can exist without the air necessarily spinning as a vortex.