2006–2007: "U" and breakthrough success

On May 23, 2006, SM Entertainment announced the addition of a new member, Kyuhyun, being the youngest member. The new thirteen member group released their new single, "U" online for free download on May 25, 2006. "U" had over 400,000 downloads within five hours of release and ultimately exceeded 1.7 million downloads, crashing the server.The single was soon followed by the release of the second semi-promo track, "Endless Moment" on May 29, 2006. The CD single "U" with a total of three tracks was officially released on June 6, 2006, eventually selling over 83,000 units. The title song "U" enjoyed number-one spots for five consecutive weeks on two of Korea's top music programs for the first time in the group's career. The song was crowned as SBS Popular Songs' Mutizen Song of the week as soon as it was released, being the first award for the group since debut. The song then stayed as Mutizen Song for three consecutive weeks on the same program. The song also grabbed top awards from M.NET's M!Countdown for two weeks. When promotions for "U" were still active, a new single, "Dancing Out" was released on July 23, 2006 as part of SMTown's annual summer album. Super Junior had been frequently appearing on various musical and variety programs to promote both of their new singles thereafter. "Dancing Out" collected two awards as soon as it was released. Because their single "Dancing Out" was a special summer single, they had their "Goodbye Special" (performing their last singles "U" and "Dancing Out" for the last time) on SBS Popular Songs on September 3, 2006. With the release of "U", Super Junior collected over seven awards in five of South Korea's music award ceremonies as 2006 came to a close, winning Best New Group and popularity awards.

An official fanclub was created for the group, E.L.F, an alphabetism derived from the phrase "Ever-lasting Friends."Since Korean fans tend to support their idols with a certain balloon color, Super Junior's official color became pearl sapphire blue.

With the start of 2007, the group began to branch out into different splinter groups. Super Junior-K.R.Y, the first subgroup of Super Junior that debuted on November 5, 2006, began to give separate performances away from the group to promote their new songs. In February arrived a second subgroup, Super Junior-T who released their first single, "Rokkugo!!!". Han Geng, who had problems with his visa and was limited to give music performances in South Korea, headed to China and began activities there. On April 19, 2007, four members of Super Junior, Leeteuk, Shindong, Eunhyuk, and Kyuhyun were injured in a car accident that deeply affected the group's schedules and progress. Being the most injured, Kyuhyun was not discharged from the hospital until four months later, therefore unable to participate in the group's single for SMTown, "Full of Happiness". Nonetheless, the cover from the former boy band H.O.T. accelerated quickly in singles charts in both South Korea and Thailand and soon became a number-one hit in Thailand's international charts a month later.