The basketball tournaments of UAAP Season 69 started on July 8, 2006 at the Araneta Coliseum and ended on October 2, 2006 also at the same venue with the UST Growling Tigers defeating the Ateneo Blue Eagles in the third game of their Finals series. The Ateneo Blue Eaglets triumphed over the FEU-FERN Baby Tamaraws to win the Juniors' championship, while the UST Tigresses won over the FEU Lady Tamaraws in the Women's Championship. In the Men's championship, the UST Growling Tigers rallied in the Finals series to beat the Ateneo Blue Eagles, 2 games to 1 to win their 19th basketball championship. Kenneth Bono of the Adamson Soaring Falcons, Bacon Austria of Ateneo and Cassy Tioseco of Ateneo won the Most Valuable Player awards.

Men's tournament

Elimination round

<section begin="Men's standings" /><section end="Men's standings" /> # [Team standings progression in the men's basketball tournament. | upload.wikimedia.org/wikipedia/commons/5/50/UAAP///Season///69///graph.PNG]

Rivalry games

These are the results of the different rivalry games:

Third–seed playoff

Bracket

<section begin="Men's bracket" /><section end="Men's bracket" />

Semifinals

In the semifinals, the higher seed has the twice-to-beat advantage, where they only have to win once, while their opponents twice, to progress.

(1) Ateneo vs. (4) Adamson

The Ateneo Blue Eagles has the twice-to-beat advantage.

(2) UE vs. (3) UST

The UE Red Warriors has the twice-to-beat advantage.

Finals

Awards

<section begin="Men's awards" />

Statistical leaders

Suspensions

Women's tournament

Elimination round

<section begin="Women's standings" /><section end="Women's standings" />

Second–seed playoff

Bracket

<section begin="Women's bracket" /><section end="Women's bracket" />

Semifinals

In the semifinals, the higher seed has the twice-to-beat advantage, where they only have to win once, while their opponents twice, to progress.

(1) UST vs. (4) UP

The UST Tigresses has the twice-to-beat advantage.

(2) FEU vs. (3) Ateneo

The FEU Lady Tamaraws had the twice-to-beat advantage after beating the Ateneo Lady Eagles for the second-seed, which led to a virtual best-of-three playoff series.

Finals

Awards

<section begin="Women's awards" />

Juniors' tournament

Elimination round

<section begin="Juniors' standings" /> <section end="Juniors' standings" />

Bracket

<section begin="Juniors' bracket" /><section end="Juniors' bracket" />

Stepladder semifinals

(3) UPIS vs. (4) Adamson

This is a one-game playoff.

(2) FEU-FERN vs. (4) Adamson

FEU-FERN has the twice-to-beat advantage, where they only have to win once, while their opponents twice, to progress.

Finals

This is a best-of-three playoff.

Awards

<section begin="Juniors' awards" />