During the 11th and 12th centuries the area of Chinzica, where this palazzo stands, was a rapidly growing quarter of town and many tower houses were built here. The 13th century was a time of population and building expansion and there was a race to buy land along the main streets of the quarter. The homes of the great merchant aristocracy were built facing the river, while shops and workshops of small merchants and artisans stood further behind.
The new palazzi were built by joining several of the narrow medieval tower houses into one construction. Palazzo Alliata was constructed in this way from medieval buildings built in the late 11th century with stone from the Verruca.
The Alliata family was of aristocratic origins; they came to Pisa in about the mid 12th century from Calcinaia, near the city, and rose quickly both socially and economically, thanks to maritime business, investments in Sardinia and relations with Catalan merchants.
After the Florentine conquest of Pisa (1406), the Alliatas, like many other great Pisan families, fled to Sicily taking men, goods and capital with them. Their palazzo underwent several changes in architecture and style until the final one in the 1600s, when the Florentine family Vaglienti acquired it and lived in it until 1773.