The visit to the Museum is articulated in seven sections that are different but complimentary.

"The City and the Water" illustrates through statues and important epigraphs of the lakes and city waterways. Of particular interest are the epigraphs dating from the XII century A.D. and the ten seventeenth century statues of the Savior and the apostles coming from the Mulini bridge (destroyed in 1944 by a bombing), which united the city to the neighboring Cittadella.

"Emblematic kindness" where the teachings of heraldry are displayed in a complex chivalrous code (evidencing the precious coat of arms) along with cultural changes and connections.

"The Family System" deciphers the emblems that are displayed and presented in the decorations of the Palace halls - clarifying the hidden meanings and discovering the historical events of protagonists and their symbolic representation.

"The Prince’s City" compares the prince’s political patronage artwork and the social, political and territory modifications promoted by protagonists during the Italian Renaissance. Of great importance is the "Virgilio in cattedra" in red marble from Verona (from the end of the XII century A.D. – beginning of the XIII century) originally placed in the Ragione Palace in Mantova. Studies remind us of the historical importance of this sculpture as a known symbol of the city.

"Antique worship" recreates the taste for collecting the Renaissance by displaying a variety of precious marble, partly from antique Gonzaga residences, giving the visitor the idea as to how they could be the envious Gonzaga collections of the king and emperors. At the center of the room, the graco throne called "Trono di Virgilio" is in Bardiglio marble (dating from the II century B.C.), and is presented as the great and precious work of extraordinary craftsmanship.

"The Rebirth of the Antique" collects works from different origins that testify the architectural and artistic taste from Renaissance Mantova. With the classical reinterpretations by Mantegna and Alberti, Mantova yields an urban masterpiece that can be compared to a new Rome.

"The Trophies of Mantegna", in this section, the complete series of nine frescoes painted by Mantegna between 1486 and 1492 is displayed: sixteenth century copies of the originals discovered in a house in Via Mazzini in 1926. The series, the biggest poem dedicated to antique Mantegna represents the victories of Cesare to celebrate the war virtues of Francesco II. It is considered to be a milestone in Italian art and was the most precious from the Gonzaga collection, now conserved at Hampton Court in London.

"Mantova Painting examples between 400 and 500", A significant collection of paintings and frescoes that offers a testimony to the diverse artistic influences from Lombardy, Veneto and Emilia. It replaces the image of a city where public customers and private devotion combine to make a name for Renaissance Mantova. In this section, the paintings and Mantegna school frescoes stand out like "Occasio e Poenitentia" (also available in brail for the blind) and the suggestive seventeenth century cast of the Madonna della Vittoria obtained from the original before the movement of the work to France in 1797.