Museo dell'Opera del Duomo is housed in a 13th century building in Piazza dei Miracoli, just a few metres from the Leaning Tower. The museum first opened in 1986 and was conceived as a location to contain the artefacts that had been removed from the Duomo and the Baptistry, while ensuring their protection and greater public use and accessibility.

The dilemma arose, in the wake of the July 1944 Camposanto monumentale roof fire, of how to best conserve the frescoes of the Camposanto and the relative sinopie (preliminary drawings), which had been revealed in 1974 with the first "tearing" of the overlying paintings.

From its location in the medieval convent of the same name near the river Artno, the San Matteo National Museum boasts a complete series of works by the leading 12th and 17th century Pisan and Tuscan masters and a flourishing collection of archaeological and earthenware artefacts. San Matteo is one of the most important European museums in the field of medieval art due to the quantity and the relevance of works it houses.

The Palazzo Reale National Museum is now housed in the sixteenth century palace of the same name that was designed by Buontalenti and home to the reigning families of Medici, Lorena and Savoia for centuries. The palace was renovated in 2001 to reveal spaces and joins with the adjacent buildings that comprised the estate of the grand ducal court.

The University of Pisa Museum of Natural History and Territory was founded in the early 1980s when the various universities merged their collections, transferring them to the Certosa di Calci.

Thanks to the importance and wealth of the collections, which bear witness to the four centuries of Pisan university research, this site has earned the reputation as one of the world's leading scientific museums. The earliest collections date back to the late 1500s.

The Art Gallery or Pinacoteca and the Volterra Civic Museum are located in Palazzo Minucci-Solaini. The Public Painting Gallery collection is the key to the museum, distinctive for the notable group of paintings by Florentine, Sienese and Volterran artists.
The valuable wooden panels from the Florentine and Sienese schools of art, featuring the polyptychs (painting divided into multiple sections) by Taddeo di Bartolo (Madonna enthroned with Child and Saints, signed and dated 1411) and Cenni di Francesco, share space with the panels by Signorelli (Annunciation) and Ghirlandaio (Cristo in gloria tra santi e il committente, l’abate Giusto Bonvicini).

The Volterra Etruscan Museum was founded in the second half of the 1700s with the extremely impressive collection of Mario Guarnacci and over time the museum has grown thanks to fresh findings and acquisitions.
The museum contains artefacts from the protohistoric and Villanovan period and a great number of findings from the time when Etruscan Volterra came into being, from the 4th to the 1st century B.C. There are also a number of 4th and 1st century B.C. Hellenistic materials on display.

The Diocesan Museum of Religious Art in Volterra contains collections of works originating from the Duomo (Cathedral) and the churches of the diocese: paintings, sculptures, goldsmith art, furnishings, manuscripts, religious hangings and the only surviving marble of the 14th century monuments of the Cathedral with works by Tino di Camaino, Angolo di Venura and Agostino di Giovanni.

The "Giovanni Alberto Agnelli" Piaggio Museum was founded in 2000 to conserve the historical memory of the great metal-mechanical company of Pontedera.

It is located in the artfully renovated former ‘Attrezzeria’ (tool shed), one of oldest of the premises’ structures.

The permanent exhibition is divided into three collections; Vespa, Piaggio and Gilera. Between various types of vehicles, motors and mechanical parts, it comprises over one hundred models that have contributed greatly to the history of Italian and international transport.

The aim of the Alabaster Eco-museum is to exhibit more than just a simple collection of objects. Instead it displays an entire territory, its history and its chief economic resource. This museum is distinctive and differentiated from the regular museums for its exhibition of time and space: it is a museum of time due to its focus on particular and defined historical sectors, while following an extensive period spanning from the past right to the present day; a museum of space because the ecomuseum formula is correlated to the particular geomorphological, environmental features.

The Museum of the Pieve, or small church, of Bientina has been open since 1993 and houses one of the most beautiful collections of religious accessories in noble metal dating back to between the 16th and 18th centuries inclusive.

The display consists of more than 120 objects, including candlesticks, chalices, monstrances, reliquaries, vases and lamps produced by the most renowned silversmiths of the Lucchese, Pisan, Florentine, Neapolitan and French schools.

The rooms of Palazzo Pretorio are home to the Russian Icon Museum, which was founded when a collection was donated by Francesco Bigazzi, a journalist originally from Peccioli and the long time correspondent from Poland and Moscow.

The first section of the museum is devoted to the earliest icons which represent the numerous and various schools of Russian iconography, from the schools of Moscow to those of Kiev or Kazan. It then passes to the more recent icons, such as those of the Bigazzi Collection, merging ancient spirituality with modern mentality.

The centre is housed in the Villa Comunale Baciocchi. The research methods used, the zones explored and the geological features of the Valdera are illustrated by means of explanatory panels that offer a split view of the presences in the zone through Prehistory and during the Etruscan, Roman and Medieval eras.

The Capannoli Zoological Museum is set up in the rooms of Villa Baciocchi, a late Baroque building surrounded by a public park featuring exotic and age-old plants. The attraction comprises a permanent exhibition of a principally educational nature directed both at a school target group and at all those who love and respect nature and animals.