Clone stormtroopers were stormtroopers created through cloning using various genetic donors, notably the Mandalorian warrior Jango Fett, whose DNA was the basis for the clone trooper army during the twilight of the Galactic Republic. After the Clone Wars, Emperor Palpatine reorganized the clone soldiers into Imperial stormtroopers within his newly established Galactic Empire. Besides the cloning program on Kamino, where the Republic's army of clones originated, the Empire also produced clone stormtroopers utilizing Spaarti cloning cylinders from Arkanian Microtechnologies and the GeNode initiative.
Following a failed uprising on Kamino, the Stormtrooper Corps experienced increased diversity; even though the 501st Legion successfully defeated a force of clone troopers resisting Imperial rule, Palpatine determined that the Empire should no longer depend exclusively on genetically-identical fighters. Subsequently, clone stormtroopers were created from new genetic sources, reducing the proportion of Fett-based clones within the Imperial Military. As time passed, the Empire relied more and more on recruitment and conscription, using naturally born Humans to augment the clone forces in the Stormtrooper organization.

In the final years of the Galactic Republic, Count Dooku hired the Mandalorian bounty hunter Jango Fett to act as the genetic blueprint for an army of clone troopers on the planet Kamino. Created for combat and obedience, the clones constituted the Grand Army of the Republic, which fought against the Separatist Droid Army of the Confederacy of Independent Systems throughout the Clone Wars. During this galaxy-wide conflict, the clone shock troopers of the Coruscant Guard were nicknamed "stormtroopers" as they acted as military law enforcers implementing martial law on Coruscant. Their presence in the Republic's capital served as a highly visible symbol of the planet's enhanced security measures, becoming the most prominent component of the Homeworld Security Command.

The designation "stormtrooper" was officially applied to all clone soldiers in 19 BBY after the Republic was transformed into the first Galactic Empire under Emperor Palpatine, leading to their designation as "clone stormtroopers." The newly established Stormtrooper Corps functioned as the Emperor's elite military branch throughout the period of the New Order, utilizing clones derived from the same genetic source that had produced the Republic's clone army.
The Galactic Empire continued to use the same military force that had enabled Palpatine—the public identity of the Sith Lord Darth Sidious—to seize absolute control of the galaxy's government. While most clone soldiers continued to be produced in the cloning centers of Kamino, the Empire also maintained its relationship with Arkanian Microtechnologies, a corporation that employed Spaarti technology to create fully grown adult clones in a single year. With a few exceptions, the vast majority of stormtroopers were clones, created through Kaminoan and Arkanian methods.

Clone stormtroopers were vital to the Empire's success in its early years, and they retained the Phase II clone trooper armor that they had customized with unit colors and markings during the Clone Wars. As the Imperial emphasis on uniformity increased, the stormtroopers reverted their clone armor to a standard white, highlighting the Empire's focus on uniformity and obedience over individuality and creativity. The clones' use of nicknames, encouraged by their Jedi commanders, also declined as Imperial officers addressed them solely by number designations, reflecting the Stormtrooper Corps' emphasis on absolute loyalty and conformity to the New Order.
Despite their new role as oppressors, the clones adapted well to Imperial duties, solidifying their image as elite soldiers to be feared. Clone stormtroopers were used to subjugate worlds, bringing their populations into compliance, as well as to hunt down fugitive Jedi and engage in operations against Separatist remnants.

A modified version of the Arkanian cloning process was developed early in the New Order, enabling the Empire to launch the GeNode program, which created clone lines of soldiers known for their efficiency and obedience. Unlike clones created through Kaminoan and Arkanian methods, GeNode clones were conditioned to believe they were natural-born humans, a deception reinforced by artificial memories and complete names. As a result of this programming, they could not grasp the fact that they were clones, nor could they discuss cloning with other GeNode clones.
GeNode clone lines were maintained in secret facilities located in the Empire's Outer Rim. The program utilized at least four genotypes, although GeNode subjects were conditioned to be unable to recognize fellow clones from the same template. A unit of GeNode stormtroopers participated in an Imperial invasion of Kashyyyk, the Wookiee home planet, serving under the command of the Emperor's apprentice, the Sith Lord Darth Vader. The GeNode program was eventually discontinued due to instances of psychological instability among its clone subjects. Despite efforts to prevent the clones from learning their true origins, some GeNodes overcame their programming and were horrified to discover themselves surrounded by identical soldiers, leading to instances where defective soldiers killed their fellow clones in fits of rage and terror.

Although they formed the majority of the early stormtrooper ranks, in 12 BBY, a rebellion on Kamino, led by disgruntled Kaminoan cloners, revealed a secret army of clones engineered to fight against the Galactic Empire. While the Kaminoans and their rogue clone army were destroyed and the uprising suppressed, the incident convinced Palpatine that the Empire could no longer rely on a clone trooper army composed entirely of the same genotype. A wide range of genetic templates were introduced soon after the Kaminoan rebels' defeat, leading to the production of soldiers from various non-Fett sources. While the Fett clones remained a significant force within the 501st Legion, they were outnumbered by non-Fett clones, whom they referred to as the "new guys."

The Galactic Empire prohibited the creation of additional clone soldiers while maintaining its existing cloning operations at full capacity, with the locations of all facilities throughout the Empire classified and placed under military jurisdiction for security purposes. However, as the importance of clone stormtroopers gradually diminished over the years, enlisted stormtroopers increasingly filled the void. Although Emperor Palpatine and Darth Vader both personally favored clones as soldiers, the Empire began to gradually supplement its clone units with natural-born recruits due to the economic and military strain of cloning. The Kaminoan process had produced an army hailed during the Clone Wars as the greatest fighting force in galactic history, but their clones were a costly drain on resources and took a decade to mature. Arkanian technology was intended to compensate for the long growth process of Kaminoan clones, but its products fell far short of the efficiency attributed to the Grand Army of the Republic.
Given the drawbacks of the Imperial Military's reliance on cloning, the Empire had no shortage of Humans who could be recruited to serve as stormtroopers. The number of enlisted troopers increased exponentially in the decade before the Battle of Yavin, culminating in their dominance in the ranks, while clones became a rarity by 1 BBY. Commander Cody, a Clone Wars veteran, lamented the state of the Imperial Military while stationed on Kamino during the Imperial Era. Tasked with overseeing the Imperial garrison on the Kaminoan homeworld, he considered the non-clone Human stormtroopers under his command incompetent and inferior to clone troopers.
The deaths of Emperor Palpatine and Darth Vader in 4 ABY plunged the Galactic Empire into chaos and disarray following the Rebel Alliance's victory at the Battle of Endor. With no clear succession, the central government on Coruscant failed to prevent the Stormtrooper Corps from fragmenting into smaller units controlled by various warlords vying for leadership of the Empire. By 9 ABY, five years after the Imperials' defeat on Endor, Grand Admiral Thrawn launched a campaign to reunite the fractured Imperial remnants under his leadership by destroying the rebels, now reorganized as the New Republic.

To achieve his vision of a resurgent empire, Thrawn replenished the Stormtrooper Corps with a new army of clone soldiers created using Spaarti cylinders. The clones were derived from various templates, including General Maximilian Veers, Baron Soontir Fel, Corporal Terkuss of the Imperial Army, and Lieutenant Creb of the Imperial Navy. Furthermore, the stormtrooper clones were shielded from the Force through the use of ysalamiri, enabling the rapid production of clones in a matter of weeks, giving them an advantage. The creation of clone stormtroopers revitalized the Empire's depleted manpower, but the Imperial counteroffensive against the Republic was short-lived due to Thrawn's assassination by his Noghri bodyguards.

After the Galactic Civil War ended in 19 ABY with the New Republic's decisive victory, the Stormtrooper Corps survived the collapse of Palpatine's New Order, albeit as a shadow of its former self. Stormtroopers continued to exist in the decades following the Battle of Endor. However, the Empire of the Hand, the Imperial Remnant, and various other successor states of the original Empire relied heavily on the recruitment of enlisted troopers. Under Palpatine's rule, stormtrooper recruits and clones were exclusively Human. The reforms implemented by the Hand and Remnant governments allowed Non-Humans to join the Stormtrooper Corps. By 130 ABY, clone stormtroopers were virtually unknown, as the military became highly diverse, dominated by enlisted troopers from a variety of backgrounds.

Initially retaining their Phase II clone trooper armor, clone stormtroopers also kept custom insignias, colors, and attachments on their armor. As the Imperial Era progressed, the clones eventually reverted their armor to its original plain white plates, emphasizing a preference for uniformity and obedience over individuality and creativity. The standard weapons of clone stormtroopers were the DC-15S and the DC-15A blaster rifle. Clone stormtroopers would eventually transition to standard stormtrooper armor as the Imperial Era continued.