The structure of the St Mark's Basilica, though much restored and altered over the centuries, is today much the same as it was after the third reconstruction commissioned by doge Domenico Contarini in 1063 and when consecrated in 1094 under Vitale Falier. This work replaced the ancient sanctuary founded in the 9th century, when the remains of the Evangelist Mark had arrived in Venice after being smuggled out of Alexandria of Egypt.

The 11th century building has to be understood against the background of the glorious age that Venice enjoyed thanks to a long period of alliances and agreements with Constantinople. A watershed moment of this process occurred in 992 with the issuing by emperor Basil II of the "Bulla Aurea" that guaranteed Venetian merchants a clear commercial advantage over their adversaries in the Mediterranean. These privileges on the eastern trade routes were further guaranteed by the Golden Bull of emperor Alexios I Komnenos in 1082.

The reconstruction of the church dedicated to the patron saint was something that occurred too in various other Italian municipalities in the 11th century, but in the Venetian case it was a sign of the city's clear and evident admiration for the capital of the East.

The edifice is in the form of a Greek cross (i.e. a cross with all arms of equal length); triapsidal, it is preceded by an atrium. At the intersection of the barrel-vaulted arms of the cross are four large quadripartite pillars to support the weight of the building. A gallery extends along the internal perimeter on the ground floor and, parallel to it, one on the upper floor supported by columns. Finally, the church is surmounted by five hemispherical domes, connected to the load-bearing structure by four pendentives. The atrium instead is punctuated with six smaller domes and two barrel vaults.

The church's reconstruction reflected Venice's admiration for Constantinople, which in the 11th century stood as a commercial and cultural point of reference. In order to exalt its own apostolic tradition by equating it to that of the capital of the East, the model adopted for the basilica was the church of the Holy Apostles in Constantinople (Apostoleion) of the 4th century, now lost. Second in importance only to Hagia Sophia, this church had been built by the emperor Constantine (d. 337) to house the relics of the Apostles – that he had found in various parts of the empire – and was eventually to become his burial place.

During the reign of Justinian (d. 527) the church was demolished and rebuilt in the plan of a Greek cross crowned with five domes, still retaining the relics of the saints and the emperor. The architects of St Mark's, therefore, borrowed not only the plan of the Apostoleion, but also its symbolic functions: as with the church in Constantinople, the St Mark's basilica was a martyrion (a church built on the tomb of a martyr or over the place of his or her death) and a state sanctuary.

The Venetian basilica also retrieved from the Byzantine East the powerful symbolism whereby the building itself, with its architecture scanned by vertical and horizontal lines and covered lined with the gold of the mosaics, was configured as a microcosm representing for the faithful an ascent from earth to heaven.

The facade of the basilica dates from the 13th century, except for the numerous works of integration and restoration that have been necessary over the years. For its full width (62 metres), it is articulated horizontally by two orders.

The lower order is punctuated by five great splayed portals, separated by bands of columns that give access to the atrium. The upper order consists of a fully accessible balcony that features four blind arches in correspondence to the portals on the ground floor and, in the centre, to visually "prolong" the main portal, a grand loggia on which stand the bronze horses.

The atrium located between the actual interior of the edifice and the facade is a structure typical of Byzantine churches and normally is the same length as the church. However, in the case of St Mark's, the atrium – built in the course of the 13th century, that is, after the Fourth Crusade – surrounds the basilica both on the northern and on the western sides. The ceiling is entirely decorated with mosaics. It has two small cupolas and two vaults in the west arm, three small cupolas on the north side and one at the intersection the two arms. These elements of the structure of the basilica convey a decidedly "oriental" impression.