St. Mary's Church was built at McDonnell Square (now Portugal Square), which was one of several squares laid out in Toronto's 1834 'New Town Extension' plan such as Victoria Square, Clarence Square, and West Market Square.
When Bishop Alexander Macdonell asked Lieutenant Governor Sir Francis Bond Head for land to build a church, he was granted a lot on the north east corner of the garrison reserve, given in part due to it having served as an emergency cholera cemetery during the epidemics that hit York (Toronto) in 1832 and 1834.
This would only be discovered when the church foundations were being dug and human remains were uncovered.

The first St. Mary's was a small white brick building erected by Bishop Armand-François-Marie de Charbonnel.
However, due to problems with the foundation, this was taken down and a second church constructed on the foundations of the first.
It was consecrated by Bishop John Joseph Lynch in May 1860.
Eventually, structural problems developed with the second building and John Walsh, Bishop of the Diocese of London, Ontario and a former pastor of St. Mary's, engaged architect Joseph Connolly to design a new church.
The cornerstone was laid on 15 August 1881 and the dedication took place on 17 February 1889.

In demolishing the old church, workmen came upon the tomb of Capuchin Father Louis Della Vagna, St. Mary's third pastor.
Della Vagna was born in 1801 in Genoa, and before joining the Franciscans at the age of twenty-four, he had worked in his father's counting house and become fluent in English.
He preached in France and conducted missions in Ireland.
Bishop de Charbonnel had often requested he come to Canada and finally having obtained permission of his superiors, Della Vagna arrived in April 1856.
De Charbonnel immediately put him in charge of St. Mary's, but the friar died of an "Inflammation of the lungs" less than a year later on 17 March 1857.
Although only at St. Mary's a brief time, Della Vagna became known for his asceticism and strict adherence to the Capuchin rule.
He was subsequently reinterred in the vault of the newly constructed St. Mary's.
  
St. Mary Catholic School was founded with the parish in 1852 and was originally operated by the Sisters of St. Joseph and the Christian Brothers.
When the school outgrew the original structure on Adelaide Street, a new building was erected in 1918 facing McDonnell Square.
This building was expanded in 1972.
Currently, it is administrated by the Toronto Catholic District School Board, teaching Kindergarten through grade eight students.

Over time, large numbers of Poles and Ukrainians began to settle in the neighborhood around St. Mary's.
By 1960, there was a large Portuguese population and McDonnell Square was renamed Portugal Square, with a part of Adelaide Street surrounding the block renamed Portugal Square to reflect the change.
By 2012 demographics changed again with the parish "becoming more and more English as the cost of living downtown has increased."

In late September, 2012, workers discovered the church had been built atop at least one mass grave.
Press reports indicate the graves are of those who died in cholera outbreaks in 1832 and '34.
The church said it would dedicate an appropriate monument to the dead.

Some music has been recorded in the church such as jazz, pop, and classical.
Trumpeter Kenny Wheeler used St. Mary's to record his record Ensemble Fusionaire for CBC in 1976 with four other fellow Canadian musicians.
St. Mary's Church was built at McDonnell Square (now Portugal Square), which was one of several squares laid out in Toronto's 1834 'New Town Extension' plan such as Victoria Square, Clarence Square, and West Market Square. When Bishop Alexander Macdonell asked Lieutenant Governor Sir Francis Bond Head for land to build a church, he was granted a lot on the north east corner of the garrison reserve, given in part due to it having served as an emergency cholera cemetery during the epidemics that hit York (Toronto) in 1832 and 1834. This would only be discovered when the church foundations were being dug and human remains were uncovered.
The first St. Mary's was a small white brick building erected by Bishop Armand-François-Marie de Charbonnel. However, due to problems with the foundation, this was taken down and a second church constructed on the foundations of the first. It was consecrated by Bishop John Joseph Lynch in May 1860. Eventually, structural problems developed with the second building and John Walsh, Bishop of the Diocese of London, Ontario and a former pastor of St. Mary's, engaged architect Joseph Connolly to design a new church. The cornerstone was laid on 15 August 1881 and the dedication took place on 17 February 1889.
In demolishing the old church, workmen came upon the tomb of Capuchin Father Louis Della Vagna, St. Mary's third pastor. Della Vagna was born in 1801 in Genoa, and before joining the Franciscans at the age of twenty-four, he had worked in his father's counting house and become fluent in English. He preached in France and conducted missions in Ireland. Bishop de Charbonnel had often requested he come to Canada and finally having obtained permission of his superiors, Della Vagna arrived in April 1856. De Charbonnel immediately put him in charge of St. Mary's, but the friar died of an "Inflammation of the lungs" less than a year later on 17 March 1857. Although only at St. Mary's a brief time, Della Vagna became known for his asceticism and strict adherence to the Capuchin rule. He was subsequently reinterred in the vault of the newly constructed St. Mary's.   
St. Mary Catholic School was founded with the parish in 1852 and was originally operated by the Sisters of St. Joseph and the Christian Brothers. When the school outgrew the original structure on Adelaide Street, a new building was erected in 1918 facing McDonnell Square. This building was expanded in 1972. Currently, it is administrated by the Toronto Catholic District School Board, teaching Kindergarten through grade eight students.
Over time, large numbers of Poles and Ukrainians began to settle in the neighborhood around St. Mary's. By 1960, there was a large Portuguese population and McDonnell Square was renamed Portugal Square, with a part of Adelaide Street surrounding the block renamed Portugal Square to reflect the change. By 2012 demographics changed again with the parish "becoming more and more English as the cost of living downtown has increased."
In late September, 2012, workers discovered the church had been built atop at least one mass grave. Press reports indicate the graves are of those who died in cholera outbreaks in 1832 and '34. The church said it would dedicate an appropriate monument to the dead.
Some music has been recorded in the church such as jazz, pop, and classical. Trumpeter Kenny Wheeler used St. Mary's to record his record Ensemble Fusionaire for CBC in 1976 with four other fellow Canadian musicians.
St. Mary's Church, Toronto