Essential reorganization of the Church structures was performed in two stages. During the first one, 1989 –1991, the old problem of the governing and the limits of the Lithuanian Church province was regulated following the will of the Holy See. At the political turning point two hierarchs enjoyed confidence and support of most Lithuanian Catholics. Both were banished from their dioceses and not allowed to exercise their Episcopal ministry during Soviet times. These are: Cardinal Vincentas Sladkevičius and Archbishop Julijonas Steponavičius. After the start of the revival six new bishops were consecrated and apostolic administrators in all dioceses were replaced by the ordinary bishops. On December 24, 1991 archdioceses of Vilnius and Kaunas were reorganized in a way that the territory of the Church provinces would coincide with the state borders. At the same time clergy coordination institutes, like Lithuanian Bishops’ Conference and its commissions, also diocesan councils of priests started a normal functioning. The second stage of the institutional reorganization that took place in 1996 – 1997, was marked by the consecration of three more bishops and the establishment of the seventh diocese – Šiauliai – in the region greatly influenced by Soviet and proletarian ideas.

The ten year period was the time of the revival of priest seminaries in Vilnius, Telšiai and Vilkaviškis, establishment of six institutions for preparation of theologians and teachers of religion and the start of interdiocesan, diocesan and deanery catechetical, family and youth centers. Parish and retreat houses, the Church Information Center, coordination of different Caritas subdivisions, reaching even the remote places of the country, add to the quality of the changing net of the Church institutions. Other novelties were the system of intense preparation for marriage and other sacraments, started in 1997 and the incitements from the part of hierarchy in 1999 – 2000 to employ more lay people as parish assistants in order to create better perspectives for the systematic catechesis.