Marduk Institute

The Marduk Institute (マルドゥック機関, Marudukku Kikan) is the supposed selection committee that screens the global population for 14 year old children who would make suitable Evangelion pilots.

Profile
Despite various statements regarding the existence of this committee, Ryoji Kaji's investigations in Episode 15 reveal that the Marduk Institute does not really exist and is instead a dummy organization composed of 108 front companies with all Evangelion candidates being hand-picked from Class 2-A in Tokyo-3 by NERV. While not explicitly said, it appears the sole purpose of this class is to keep potential candidates safe and on-hand should they be required.

The entirety of the selection process including factors are entirely unclear. Whether Ritsuko Akagi alone has sole discretion the candidates, if Gendo Ikari and Ritsuko are involved together or if some other process is employed is unknown. Since Kozo Fuyutsuki and Chairman Keel Lorenz are listed on the board of directors of the phantom companies it is possible they have some involvement as well.

Selection of the Fourth Child
Following Shinji running away from home in Episode 04, Gendo tells Ritsuko that the Fourth Child has yet to be found as per the Marduk Institute's report. Aside from the fact that this reveals that there is a Third Child who has yet to appear in the story, Asuka and Unit-02, the conversation seems meaningless. Gendo and Ritsuko both know that Marduk is a sham and NERV picks the pilots itself. Gendo and Ritsuko (with Rei following them) are essentially in private and don't need to make the conversation up. Thus it is likely true that Toji has yet to be selected, and they must be mentioning the Marduk fiction simply because Rei is present.

This still leaves at least one question: When Toji Suzuhara is selected in Episode 17, Ritsuko picks him because a core can be configured for him. Shinji synchronizes with Unit-01 because his mother Yui's soul is in it, and Asuka synchronizes with Unit-02 because her mother Kyoko's soul is in it. The Classified Information makes it clear that the Pilot/Mother relationship is true for all Evas with the exception of Unit-00, thus Unit-03 contains the soul of Toji's mother. The timespan of Evangelion construction appears to be over a span of years in case of earlier Evangelions and only a few months for the Mass Production Evangelions. Whether they select the most suitable pilot and then use the corresponding soul, or vice-versa remains unanswered.