The seminary serves the dioceses of Kotido and Moroto. Its foundation dates back to 1967 when the first Bishop, Sizto Mazzoldi Msgr. created it to help as a recruitment ground for priests to the then young diocese of Moroto which covered the whole Karamoja region. Students came from Namaalu to Karenga. Several of the Karamojong Catholic priests went through this institution. Such priests as Fr. Simon Lokodo of Karenga-Kapedo, now member of the Uganda Parliament, Fr. Philip Lokel of Loyoro, Fr. Lotuk Samuel from Karenga. The first product was ordained in 1979, the late Fr. Thomas Logiel, who was the first Karamojong priest. Then followed others like Fr. Largo Koryang, Fr. Gabriel Koryang. The institution was as stated above, started by Bishop Sizto Mazzoldi of The Comboni Missionaries (Verona Fathers) who was a group of missionaries who had been expelled from the southern Sudan, the last Comboni Missionaries were there in 1999 when the running and the administration of the school was handed over to the diocesan clergy with the first diocesan rector being Fr. Clement Othim from Morulem.
Other students who reached to the Major seminary were Opio Kizito, Thomas Apurio, by now, a priest himself. There have been good to moderate attempts to secure this institution for future of the dioceses and other attempts.
St. Mary's Seminary Nadiket should not be confused as is often the case with The International seminary of The Apostles of Jesus, next door. It was also started by the late Bishop Sizto Mazzoldi, who co-founded The Apostles of Jesus missionary institute. The graduates from this institution unlike those from St. Mary's go on to be missionaries in other countries. They can become Brothers or priests depending on the choice of the individual.