The 1999 Illinois High School Association (IHSA) State Championship Tournaments ended the thirteenth State Championship Series conducted in Scholastic Bowl by the IHSA. It was the eighth season in which there were separate State Championship Tournaments held for small schools (Class A) and large schools (Class AA). For the third year, both Tournaments were held at the Peoria Civic Center.
Within each class, the state was divided into eight areas (Sectionals) Each sectional hosted a tournament, the winner of which advanced to the State Championship Tournament. The determination of these geographic boundaries was arbitrarily decided by the IHSA Office.
Each round was comprised of 30 toss-ups and accompanying bonus questions. The sectional tournaments and State Championship Tournament were all single elimination. Teams were randomly assigned to positions in the bracket without regard for record or performance.
The exception to the single elimination format occurred in the semifinals, where the two semifinal losers played a third place match. The top four teams earned trophies and medals for team members, coaches, principals, and activities directors. The trophies were of the design smaller than that of the athletic trophies given out by the IHSA.
- In all the years that The Latin School appeared in the State Championship Tournament, 1999 marked the only time the team was eliminated in the first match, and only the second time in the school's first eight appearances at the Tournament that it would not go home with a top-four trophy. It also marked the final match Dr. Leroy Weinbrenner would coach at the school before moving on to Waukegan. He had been head coach or co-coach (with Rob Grierson) for six seasons that included 2 State Titles.
- University High School's championship was mired in controversy when accusations came forward that one of their star players had been playing on the team for five years, in violation of IHSA By-Laws regarding eligibility. These suspicions were never officially reported, and no one ever seriously sought to launch an investigation.
- IMSA set a record in winning four consecutive State Titles, and five in their last five trips to the State Championship Tournament. This record remains intact as of 2008. IMSA dominated its opponents due largely to Peter McFerrin, Kevin Costello, and Yogesh Raut.
- MacArthur went into the final question of the semifinal needing to answer the tossup and sweep the bonus. The tossup was almost identical to a question that had been used in the previous year's Quarterfinal, and the bonus was to find the areas of four triangles given their bases and heights.