A sarcomere is the basic unit of a cross striated muscle's myofibril. Sarcomeres are multi-protein complexes composed of three different filament systems. The thick filament system is composed of myosin protein, the thin filaments are assembled by actin monomers and the elastic filament system is composed of the giant protein titin (also called connectin). A muscle cell, from a bicep, may contain 100,000 sarcomeres. The myofibrils of smooth muscle cells are not arranged into sarcomeres.

The sarcomeres are what give skeletal and cardiac muscles their striated appearance. A sarcomere is defined as the segment between two neighbouring Z-lines (or Z-discs). In electron micrographs of cross striated muscle the Z-line is appears as a series of dark lines. Surrounding the Z-disc is the region of the I-band. Following the I-band is the A-band. Within the A-band is a paler region called the H-band. Finally, inside the H-band is a thin M-line (or M-band). A-bands and I-bands were named after anisotropic and isotropic, respectively; their properties under a polarizing microscope. Actin filaments are the major component of the I-band and extend into the A-band. Myosin filaments extend throughout the A-band and are thought to overlap in the M-band. The giant protein titin (connectin) extends from the Z-disc of the sarcomere, where it binds to the thin filament system, to the M-band, where it is thought to interact with the thick filaments. The Titin protein (and its splice isoforms) is the biggest single protein found in nature. It provides binding sites for numerous proteins and is thought to play an important role as sarcomeric ruler and as blueprint for the assembly of the sarcomere. Several proteins important for the stability of the sarcomeric structure are found in the Z-disc as well as in the M-band of the sarcomere. Actin filaments and Titin molecules are cross-linked in the Z-disc via the Z-disc protein alpha-Actinin. The M-band proteins Myomesin as well as M-protein crosslink the thick filament system (Myosins) and the M-band part of Titin (the elsatic filaments). The interaction between actin and myosin filaments in the A-band of the sarcomere is responsible for the muscle contraction (sliding filament model).

Upon muscle contraction, the A-bands maintain their length (1.6 micrometer in mammalian skeletal muscle) whereas the I-bands shorten.

The A-band, I-band and Z-line are the only components visible at the light-microscope level.

The protein tropomyosin covers the myosin binding sites of the actin molecules in the muscle cell. To allow the muscle cell to contract, tropomyosin must be moved to uncover the binding sites on the actin. Calcuim ions bind with troponin molecules (which are dispersed throughout the tropomyosin protein) and alter the structure of the tropomyosin, forcing it to reveal the cross bridge binding site on the actin. The concentration of calcium within muscle cells is controlled by the sarcoplasmic reticulum, a unique form of endoplasmic reticulum. Muscle contraction ends when calcium ions are pumped back out of the sarcomere.

Skeletal muscle only contracts when an impulse is received from a motor neuron. During stimulation of the muscle cell, the motor neuron releases the neurotransmitter acetylcholine which travels across the neuromuscular junction (the synapse between the terminal button of the neuron and the muscle cell). The action potential then travels along T (transverse) tubules until it reaches the sarcoplasmic reticulum; the action potential from the motor neuron changes the permeability of the sarcoplasmic reticulum, allowing the flow of calcium ions into the sarcomere. The outflow of calcium allows the myosin heads access to the actin cross bridge binding sites, permitting muscle contraction.

At rest, the myosin head is bound to an ATP molecule in a low-energy configuration and is unable to access the cross bridge binding sites on the actin. However, the myosin head can hydrolyze ATP into ADP and an inorganic phosphate ion. A portion of the energy released in this reaction changes the shape of the myosin head and promotes it to a high-energy configuration. Through the process of binding to the actin, the myosin head releases ADP and inorganic phosphate ion, changing its configuration back to one of low energy. As the filament of actin moves away from the myosin head and back toward the center of the sarcomere, the myosin head is unable to preserve its bond with the actin. After cross bridge dissociation, ATP binds with the myosin head and the head is ready for another cycle of muscle contraction.

Most muscle cells only store enough ATP for a small number of muscle contractions. While muscle cells also store glycogen, most of the energy required for contraction is derived from phosphagens. One such phosphagen is creatine phosphate, which is used to provide ADP with a phosphate group for ATP synthesis in vertebrates.