The foundation stone for this church was laid on the 24^th of November, 1594. Archbishop Rev. Fr. Aleixo de Menezes consecrated the church, on its completion on the 15^th of May 1605. However, it was only raised to the status of “minor Basilica” in 1946.The three-storied structure stands 75ft wide and 78½ft tall. The façade of the church, though un-plastered, is a magnificent example of baroque architecture. It combines elements of Doric, Ionic and Corinthian design, and is divided into four parts.The lowest section has three doors set into it, a large one in the middle with two smaller ones flanking it. The second section has three square windows whose positioning corresponds to that of the doors. The third section has three circular windows whilst the last section forms a quadrangle, lavishly decorated with arabesque. This quadrangular pediment also has “IHS” carved into it. This is the Jesuit emblem and stands for “Iesus Hominum Salvator”, which is Latin for, “Jesus, Saviour of Men”. All the sections have carved basalt pillars. The basalt was mined from Bassein in the North of Goa.

The interior of the Basilica measures 83ft in length, 51ft in width and 61ft in height. It is laid out in the orthodox cruciform fashion with a single nave and transept. The ceiling was once vaulted, but has since been replaced with a simple wooden one. The main altar measures a massive 54ft by 30ft. The interiors, while being furnished with the best of materials show a remarkable simplicity typical of Renaissance design.The Basilica contains two chapels, three altars, a sacristy and a choir loft. There is also a belfry at the back. The door through which one enters stands beneath the choir loft. To the right is an altar which is dedicated to St. Anthony and to the left is a well-carved statue of St. Francis Xavier. On the northern wall of the nave is the cenotaph of Dom Jeronimo Mascarenhas. He was the Captain of Cochin and his estate made possible the construction of the Basilica.
 
The columns which support the choir loft bear plaques inscribed in Portuguese and Latin detailing the dates of the Basilica’s construction and consecration. In the transept are two altars which flank the main one. They are highly carved and decorated and are dedicated to St. Michael and Our Lady of Good Hope.The main altar is extremely well carved and gilded. It is backed by an ornate reredos which stretches from floor to ceiling, its baroque carvings in sharp contrast to the classically plain design of the Basilica. The reredos has within it a large statue of St. Ignatius of Loyola protecting the Infant Jesus. His eyes are raised to a carved disc, once more bearing the Jesuit emblem of “IHS”. Above this medallion is a depiction of the Holy Trinity, i.e. The Father, The Son and The Holy Spirit.
 
On the northern side of the transept is the Chapel of the Blessed Sacrament. On the southern side is the Chapel of St. Francis Xavier. Adjoining this chapel is a corridor leading to the sacristy, accessed by a marvellously carved wooden door. It is a vaulted wooden structure ending in an apse. In this reposes an altar which has an iron chest containing the Golden Rose which was bestowed upon the Se Cathedral by Pope Pius XII.The walls are hung with paintings of the saints and the sacristy also contains a beautifully carved chest of drawers. Near the iron chest is a painting of the relics of St. Francis Xavier, done about 100 years ago.

The tomb of the great saint, rests beneath a shower of gilt stars. It has three parts: the altars, the Florentine mausoleum and the silver casket. There are four altars, one on each of the four sides of the tomb. They are constructed of reddish jasper with white strips which are ornamented with flourishes and fringes. There are two Cherubim in each corner. They are made of pure alabaster. In the centre of each altar’s frontispiece there is an emblem in bold relief. Above the altars is a quadrangle of spotted jasper. On all four sides are bronze plaques depicting scenes from the life of the saint.
 
In the first scene we see St. Francis preaching to the Malaccan people. Above the panel is a bronze sun disc and two alabaster angels holding a bronze banner inscribed with the words “Nox inimical fugat”. The second scene shows St. Francis baptisting the Malaccans with his right hand and holding a crucifix in his left. The bronze sun is at it’s zenith above this plaque and the banner held by the angels reads “Ut vitam habeant”. The third scene depicts St Francis being attacked by the Moro islanders with stones and arrows. The bronze medallion shows a lion in a storm and the banner reads “Nihil horum vereor”. The fourth plaque shows the death of St. Francis on the island of Shangchaun surrounded by his disciples. The medallion depicts the setting sun and the banner reads “Major in occasu”. Taken together these four Latin phrases can be roughly translated to mean “I drive away the enemy of the night, that they may have new life and fear not the great setting of the sun”

Above this quadrangle is a balustrade of jasper and it is on this balustrade that the silver coffin rests. There are 32 silver plates which form the four sides of the casket. The scenes that they depict are as follows:

• Francis lies on the ground with his arms and legs tied, but the cords are miraculously broken.
• Francis kisses the ulcer of a patient lying in a Venetian hospital.
• He is visited by St. Jerome as he lies ailing in the hospital of Vicenza.
• A vision about his future apostolate.
• A vision about his sister’s prophecy regarding his fate.
• He saves the secretary of the Portuguese Ambassador while crossing the Alps.
• He lifts a sick man who dies after receiving communion.
• He baptizes the people in Travancore.
• He resuscitates a boy who drowned in a well at Cape Comorin
• He miraculously cures a man full of sores
• He drives away the Badagas in Travancore
• He resuscitates three persons: a man who was buried at Coulao; a boy about to be buried at Multao and another child.
• He takes money from his empty pockets and gives to a Portuguese beggar at Malyapore.
• He effects a miraculous cure.
• A crab restores his crucifix which had fallen into the sea.
• He preaches in the island of Moro.
• He preaches in the sea of Malacca and announces victory against the enemies.
• He converts a Portuguese soldier.
• He helps the dying Vicar of Malacca.
• Francis kneels down and on his shoulders there rests a child whom he restores to health.
• He goes walking from Amanguchi to Meaco.
• He cures a dumb paralytic in Amanguchi.
• He cures a deaf Japanese person.
• He prays on the ship during a storm.
• He baptizes three kings in Cochin.
• He cures a religious person in the College of St. Paul.
• Due to lack of water, he sweetens the sea water, during a voyage.
• The agony of Francis at Sancian.
• After his death he is seen by a lady according to his promise.
• The body dressed in sacerdotal vestments is exposed for public veneration.
• Francis levitates as he distributes communion in the College of St. Paul.
• The body is placed in a niche at Chaul with lighted candles.

The casket is topped by a cross standing on a pedestal with the figures of angels, one on either side. The angel placed near where his head rests bears a heart with a halo, whilst the one near his feet has the motto “Satis est! Domine, satis est” which means “It is enough, Oh Lord, it is enough”During the time of the exposition, the plates on the side of the silver casket are removed so that devotees may see the “intact” remains of the saint through the glass urn. The glass urn was put in place after the exposition in 1954, when it was decided that the relics should no longer be directly touched. It was made in the Casa Brandizzi in Rome and the relics were placed inside with all ceremony in 1955, before the whole was placed into the silver casket.