The complex was built in the 18th century by Father Luis Felipe Neri de Alfaro, who, according to tradition, was called upon by a vision of Jesus with a crown of thorns on his head with blood on his face and carrying a cross.

[4] Atotonilco is located fourteen km outside the town of San Miguel de Allende in an area that is a combination of dry grassland and desert studded with thistles, sweet acacia and mesquite trees.

[5] Today, thermal waters still rise up from the ground only one km from the sanctuary, and another spring at the community entrance has been covered by an artificial cave and is used as a spa called Balneario La Gruta.

[8] The main entrance is also simple under a "mixtilineo" arch that faces east, towards Jerusalem, giving the entire complex an east-west orientation.

The main church is a single nave without a cupola, lined on the north and south flanks by chapels and chambers.

[10] On the north side of the nave, there are the new sacristy, the Rosary Chapel, the chambers of Father Neri, the Belen Chapel/Baptistery and the Reliquary Room.

[11] The walls and ceilings of the interior are nearly entirely covered in mural work, sculpture, inscriptions and oil paintings in a style called Mexican folk Baroque, although indigenous influence can be seen.

[10] Most of the mural work was done by Antonio Martínez de Pocasangre with some done by José María Barajas over a period of thirty years with almost no free space left among the numerous images.

In the highest part, Jesus appears crowned and with a cape carrying a cross, and blessing certain chosen people with his right hand.

On the north side, Pilate appears again but the Jewish judges stay outside the Roman magistrate's house because they are observing Passover.

[18] At the presbytery section, at the location of the main altar, can be found a depiction of Palm Sunday, the crucifixion, and death of Jesus.

[14][18] The line along the ceiling of the nave is supposed to trace the path from sin and Hell to the "glory of God's presence.

The vault contains a conjunction of angels that sing the arrival of the Messiah, peace, and a group of shepherds who come to adore the child.

Prior to the restoration of the Camarín de la Gloria (Chamber of Glory), the oils on canvas covered medallions on the walls.

There is no direct access to this chapel from the main nave of the church; it is necessary to enter from the current sacristy or through the Capilla de Soledad.

The north wall contains a triptych where a dying man is surrounded by a priest, a guardian angel, and several demons vying for his soul.

This chapel contains an image of a resuscitated Jesus but still reclined which is notable for the bloody face and the number of precious stones that have been placed on it.

It was originally painted by Pocasangre, but little remains due to subsequent re-paintings and the enclosure of the space when the "Casa de Ejercicios" or meditation room was added.

[31] The architecture and decorative features reflect the doctrine of Saint Ignatius of Loyola,[3] as it was built with the principles of the Counter-Reformation in mind.

The sanctuary's role as a site for penance, according to the exercises of Ignatius Loyola, began in 1765 with 25 people participating and directed by Father Neri.

[10] The sanctuary has been one of the principal places in Mexico to practice the spiritual exercises of Ignatius of Loyola, which include mortification of the flesh through flagellation and fasting.

It is one of 33 weeks out of the year when visitors, mostly from the center and north of the country, visit the Casa de Ejercicios to perform penance.

Today, and each year on the Saturday prior to Holy Week, it travels to San Miguel and returns to Atotonilco on Thursday night.

[35] Chichimecas came to this particular place to perform penance rites, puncturing themselves with maguey thorns and washing away guilt in the thermal springs.

While resting under a mesquite tree where the sanctuary is now located, he dreamt of Jesus wearing a crown of thorns and carrying a cross.

[37] A different version of this story states that Father Neri was here due to his ill health and was assisting at a small church called the Capilla de San Miguelito, which is still found on the banks of the Laja River.

At that time, the native Guachichiles and Pames were not completely converted to Christianity and considered the thermal springs in the area sacred and medicinal.

[38] Father Neri bought the entire Hacienda de Atotonilco to build the sanctuary and to have enough productive land to support it.

[35] When Father Neri traced the layout of the church, it was the morning of May 3, the day of the Holy Cross, when he is said to have seen three rainbows, one to the east, one to the north and one to the south, leaving the west free.

All that was missing at that time was the Santa Escuela annex, the new sacristy, some hallways and the chaplain's house, as well as various sculptures, altars and oil paintings.