When Herzegovina became part of the Austro-Hungarian empire, Pope Leo XIII took steps to establish dioceses (1881) and appoint local bishops. This included transferring parishes administered until then by the Franciscans to diocesan clergy. The friars resisted, and in the 1940s Franciscan provinces still controlled 63 of 79 parishes in the dioceses of Vrhbosna and Mostar. In the 1970s, friars in Herzegovina formed an association of priests to encourage popular opposition to diocesan parish takeovers. A 1975 decree by Pope Paul VI, Romanis Pontificibus, ordered that Franciscans to withdraw from most of the parishes in the Diocese of Mostar-Duvno, retaining 30 and leaving 52 to the diocesan clergy. In the 1980s the Franciscans still held 40 parishes under the direction of 80 friars.
In 24 June 1981, six children in the town of Medjugorje, Yugoslavia (today, Bosnia-Herzegovina), said they had seen an apparition of the Blessed Virgin Mary and that these apparitions were continuing. The village began to attract pilgrims.
On 11 January 1982, Pavao Žanić, Bishop of Mostar, within whose jurisdiction Medjugorje lay, established a commission to look into the matter. When three days later, on 14 January 1982, three of the seers advised him that the "Madonna" supported the Franciscans, Bishop Zanic began to be concerned that they were being guided more by their Franciscan advisors than by the Blessed Virgin.
In November 1983, the Congregation for the Doctrine of the Faith asked the bishop if the Commission had come to some conclusions. Bishop Žanić sent a study in which he said the apparition could not be from God because of the "disorder and disarray" it caused, and that it was probably a hoax because "from the outset one can notice that the children have sometimes lied".
In 1984 Bishop Žanić decided to extend the first Commission and expanded its membership to fifteen: 12 priests and 3 medical experts. They held seven meetings in all. This second commission completed its work in May 1986. Eleven members determined that the events at Medjugorje were Non constat de supernaturalitate (i.e., It is not confirmed to be of supernatural origin), 1 abstained, 1 accepted ‘in nucleo’ and 2 voted against the finding.) The Commission prepared a draft “Declaration” in which were listed the “unacceptable assertions” and “bizarre declarations”, attributed to the curious phenomenon. The Commission also stated that further investigations were not necessary nor the delaying of the official judgement of the Church. The bishop duly informed the Bishops’ Conference and the Holy See.
The current ordinary, Bishop Ratko Perić issued a statement on February 27, 2017 saying: "Considering everything that this diocesan chancery has so far researched and studied, including the first seven days of alleged apparitions, we can say: there have been no apparitions of Our Lady in Medjugorje"
With the possible breakup of Yugoslavia, many Croat church leaders saw the new Marian cult in Herzegovina as both an aid to anti-communist efforts and a potential focus for Croat nationalism in both Croatia and Bosnia-Herzegovina. As the Medjugorje events had exceeded the scope of a local event, in January 1987, upon the suggestion of the Congregation for the Doctrine of the Faith, Cardinal Kuharić and Bishop Žanić made a joint communiqué in which they announced the formation of a third Commission under the direction of the Bishops Conference. The bishops would both review the work of the previous commissions and conduct its own inquiry. The Conference instructed that pilgrimages should not be organized to Medjugorje on the basis of its being supernatural. In July Bishop Žanić forbade any priests who organized pilgrimages or came there ascribing a supernatural character to the events, to celebrate Mass in his diocese, and this until the Commission of the Bishops’ Conference completed its inquiry.
On 10 April 1991, the Yugoslav Episcopal Conference issued at Zadar its own Non constat de supernaturalitate declaration stating that: "On the basis of the investigations so far it can not be affirmed that one is dealing with supernatural apparitions and revelations." Recognizing that people travelled to medjugorje, the bishops made provision for appropriate pastoral care.
In response to an inquiry from a French bishop, in March 1996 then Archbishop Tarcisio Bertone, Secretary of the Congregation for the Doctrine of the Faith under Cardinal Ratzinger, stated that official pilgrimages to Medjugorje, understood as a place of authentic Marian apparitions, are not permitted to be organized either on the parish or on the diocesan level. The following June, in response to reporters' questions, Joaquin Navarro-Valls, spokesman for Holy See Press Office, clarified that Archbishop Bertone was referring specifically to official pilgrimages. Catholic parishes and dioceses may not organize pilgrimages to Medjugorje, as that might give the impression of a canonical endorsement.
In 1993 Bishop Žanić retired at the age of 75 and was succeeded by his coadjutor, Bishop Ratko Perić. On 2 October 1997, Perić wrote: that he was convinced that the events alleged at Medjugorje were no longer non constat de supernaturalitate (that their supernatural nature is not established) but constat de non supernaturalitate (it is not of a supernatural nature). In May 1998, in response to an inquiry from Bishop Gilbert Aubry, Bishop of Saint-Denis on Reunion Island, Archbishop Bertone cited the previous 1991 finding of non constat de supernaturalitate by the Yugoslav Bishops Conference, and noted that since the division of Yugoslavia, jurisdiction now lay with the Episcopal Conference of Bosnia-Herzegovina. Bishop Perić's statement must be considered the expression of the personal view of the Bishop of Mostar, who, as Ordinary of the place, always has the right to express what is, and remains, his personal opinion.
On 17 March 2010, the Holy See announced that, at the request of the bishops of Bosnia Herzegovina, it had established a commission, headed by Cardinal Camillo Ruini, to examine the Medjugorje phenomenon.
On 21 October 2013, the Apostolic Nunciature to the United States communicated, on behalf of the Congregation for the Doctrine of the Faith, that, in the light of the 1991 Zadar declaration about the Medjugorje events, Catholics, whether clergy or laypeople, "are not permitted to participate in meetings, conferences or public celebrations during which the credibility of such 'apparitions' would be taken for granted". The letter was sent to every diocese in the U.S. as Archbishop Müller of the CDF wanted the U.S. bishops to be aware that Ivan Dragicevic, one of the “so-called visionaries” of Medjugorje, was scheduled to give presentations at parishes across the country and was anticipated to have more apparitions during these talks. Because the commission established in 2010 was still in the process of its investigation, the CDF determined that the judgment of the Yugoslavian bishops which precluded such gatherings remain in force.
On 18 January 2014, the Vatican commission set up in 2010 to study the Medjugorje question was reported to have completed its work, the results of which it would communicate to the Congregation for the Doctrine of the Faith.
On 6 June 2015, Pope Francis, referring to the Congregation for the Doctrine of the Faith, told reporters "we’ve reached the point of making a decision and then they will say.”
On 11 February 2017, Pope Francis named Bishop Henryk Hoser of Warszawa-Praga in Poland as his special envoy to Medjugorje, charged with investigating the pastoral situation in Medjugorje and the needs of pilgrims.
Until such time as the Congregation for the Doctrine of the Faith releases its findings, the 1991 determination of the Yugoslav Bishops Conference of non constat de supernaturalitate ("It is undetermined at this time if it is of supernatural origin") still stands, and the Holy See considers this judgement still operative. Traditionally, there have been one of three determinations with regard to apparitions: 1. Constat de supernaturalitate (Determined to be supernatural) (approved) 2. Non constat de supernaturalitate (Not determined to be supernatural) (Neither approved or condemned - not determined - neutral) 3. Constat de non supernaturalitate (Determined not to be supernatural) (condemned) Until such time as the Vatican commission's findings are revealed and approved by the pope, the "not determined" ruling remains in effect.
On the basis of the letter of 21 October 2013, which refers to the letter of February 2013, Colin B. Donovan of EWTN remarked: "These 2013 letters clearly represent a change of pastoral attitude on the part of the Holy See, one which began before the end of the pontificate of Pope Benedict and which has now been affirmed by Pope Francis. An attitude of seeming tolerance has been replaced with a firm call for acceptance of the ecclesiastical judgments made to date, or at least publicly acting in accordance with them." He added: "Catholics on both sides of the issue should exercise prudence and charity in speaking of it. Medjugorje is not a litmus test of orthodoxy, though every Catholic will have a moral obligation to accept the judgment of Rome, in the manner Pope Benedict XVI explained, when it is rendered."
Also regarding the October 2013 letter, Jimmy Akin of Catholic Answers, when asked "what does this tell us about how the Church is likely to rule on Medjugorje?" replied, "Not a great deal. It certainly is not an encouraging sign for those who would want to see Medjugorje approved. On the other hand, sticking with the existing policy and applying its logic more rigorously is not a change of substance and does not tell us anything in particular about what the ultimate ruling is likely to be. The current Medjugorje commission is expected to deliver its findings to the CDF for evaluation, and, after the CDF has had a chance to study them, the results will be presented to the pope. It will be the pope who makes the final decision. Sticking with the current policy at the present time does not tell us anything, one way or another, about what that decision will be."