There are two marching bands and four concert bands at Juan Seguin High School. The Cougar Marching Band is comprised of all students in the Juan Seguin band program. Membership in the Varsity Marching Band is achieved by audition only. Students are placed in either Wind Ensemble, Symphonic Winds, Symphonic Band, or Concert Band based on their current level of musical ability.

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The Cougar Marching Band performs in the stands and at pregame of all home football games. All students who are enrolled in a band class perform with the Cougar Marching Band. There are no alternates in the Cougar Band. Rehearsals are from 3:30 until 4:30 Monday, Tuesday, and Thursday during the Fall.

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The Varsity Marching Band performs in the stands and at halftime of all away football games. Students must audition during band camp to earn a spot in the Varsity Band. In addition to performances at away football games, the Varsity Band performs in several marching competitionsincluding UIL marching competition. In 2005, the Varsity Band was a state marching semi-finalist. Rehearsals are from 3:30-6:00 Monday and Tuesday, 3:30-4:15 Wednesday, and 3:30-5:45 on Thursday during the Fall.

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The Wind Ensemble is the premiere performing group at Juan Seguin High School. Students in this ensemble have demonstrated a high level of mastery on their instrument and are capable of performing music literature at a high level. The group regularly participates in UIL concert band festival and has received straight first division ratings for the last 4 years.

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The Symphonic Winds are comprised of students who are proficient on their instrument, but may not have developed to the level of a Wind Ensemble member. Students in this ensemble perform music at a level appropriate for their development. The group regularly participates in UIL concert band festival and has recevied first division ratings regularly since the school opened in 2002.

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The Symphonic Band is comprised of students who are proficient on their instrument, but may not have developed to the level of a Symphonic Winds member. Students in this ensemble perform music at a level appropriate for their development. The group regularly participates in UIL concert band festival.

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The Concert Band is comprised of students who are still developing on their instrument. In this setting, directors are able to give individual attention to students. The goal each year is for all students to be a member of the Symphonic Band by the end of the year. The Concert Band does not participate in UIL concert band festival.