The diocese of Clogher, like all Irish dioceses, goes back to the great reforms of the twelfth century. These reforms, spearheaded by St Malachy and St Laurence O’Toole, set up the structures of the Church in Ireland as we know them today. The extent of each diocese was initially agreed by fixing a number of boundary points and was then worked out in detail. The organisation of parishes within the diocese then followed, and by the year 1300 the plan was in place.

Each diocese was given a name, nearly always from an ancient site. The nomination of Clogher, rather than Clones or Devenish, seems to stem from the connection with St Patrick and the concern of the reformers to promote episcopal rather than monastic control. A ninth century life of St Patrick describes him establishing his thréanfhear (strong man) Macartan at Clogher. St Macartan duly became the patron of the new diocese, and the bishop and his cathedral chapter were expected to live at the new episcopal centre.

The savage wars of the sixteenth and seventeenth centuries brought the total destruction of the patrimony of the Catholic Church in Ireland. In the diocese of Clogher only the Lough Derg pilgrimage maintained unbroken continuity throughout the centuries of persecution. Bishop MacNally, the founder of the Cathedral, described the situation in 1853, in the robust language of the day:

The great and long-continued persecution of the Catholics in this country weighed incomparably more heavily on the Catholics of Ulster than upon those of the other provinces. In one persecution after another the churches, the religious institutes, the clergy and the whole people were totally stripped of all their possessions and such as escaped ruin were chased from the towns into mountainous districts, and as far as it was possible they were left incapable of acquiring property of any kind. All the temporal goods of the diocese were handed over in 1570 by Queen Elizabeth of England to the unfortunate Miler Magrath, who, after being promoted by St Pius V to the bishopric of Down, apostasized publicly from the faith. Thus gradually the cathedral, the churches and all the great church revenues of this episcopal see were passed into the hands of the heretics where they remain to this day. Since the time of these misfortunes we have no cathedral church, nor even cathedral services, properly speaking.

In this diocese we are gradually recovering from the deplorable state of things that we have mentioned. There are still people alive who remember that in their time there was scarcely a Catholic church or chapel in the entire diocese so that in all the seasons of the year our poor people had to gather in the open air under the heavens to hear Mass, with a covering only for the altar and for the priests during the celebration of the Divine Mysteries. After I was ordained priest, I myself had to celebrate Mass in this way in one of the districts of this very parish in which I now reside.

The bishop goes on to say that he was at that time (1853) living in the parish of Monaghan and that the parish church was joined to his residence. This was the old church in the cemetery at Latlurcan, which is still standing although long since out of use.

The decision to build the Cathedral came five years later. On 3 January 1858, at a meeting of the Catholics of Monaghan, with Bishop MacNally presiding, it was formally resolved that a new church at Monaghan was urgently necessary. An eight-acre site was purchased by the bishop from Humphrey Jones of Clontibret for £800, and an architect, James Joseph McCarthy of Dublin, was employed to draw a design. On 21 June 1861 the foundation stone was solemnly laid in the presence of most of the bishops of Ireland. By April 1862 the work was under way. According to a contemporary account:

…..it was not unusual to see 400 or 500 horses and carts, filled with lime, stone and sand, arrive at the building together; the horses and carts and men having been supplied gratuitously by the people of the various parishes surrounding.

The stone for the building came from a large quarry of grey and cream coloured limestone near what is now Old Cross Square.

When Bishop MacNally died in 1864 the walls were already 32 feet above the levels of the foundations. In 1865 the work resumed under his successor Bishop James Donnelly, and continued under his personal and unremitting direction until completion in 1892. On 21 August of that year the Cathedral was solemnly dedicated, again in the presence of the bishops of Ireland. A week later, on 28 August, there was a special celebration for the people
of the parish.

When the architect McCarthy died in 1882, his successor was the Cavan man, William Hague. Hague was responsible for the design of the spire and the gate lodge.

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