The oldest remains found in this town date from ; they were found in the caves called Txotxinkoba and Jentilkoba. They were used for burials, and the dead were buried together as it was customary in that period.
There are, though, no written documents until . In his book about the history of Bizkaia, Iturriza mentions that the area was called Ibaibaso. It apparently changed its name in the Xth century. After the battles against the French -always according to Iturriza-, the town took the name of Gizaburuaga, which meant .
People did not settle in the area until the Xth-XIth centuries, when and people gathered in groups to live in a certain place.
1325 is the exact date. It is believed that until then the town was part of the fief of Lekeitio, and that when and the economy flourished, the urge for independence increased; and that, as a result, Gizaburuaga became a church subject to Lekeitio in the Lower Middle Ages and a parochial district in the Upper Middle Ages.
The first application to separate from dates from 1454; the inhabitants of Gizaburuaga applied to the Pope. The archbishopric did not grant them independence, because the church made great economic profits from Gizaburuaga and hence a separation was not convenient. Not happy with this, the town started acting independently and as a result it was excommunicated in 1460.
After many arguments, the Bull of Gizaburuaga independence, and it also made Amotoro independent. This bull gave the town the rights to have a baptismal font and to heal the parishioners´ souls, to have priests and to carry out burials, and so the Council of Lekeitio was forced to appoint a priest for Gizaburuaga and to redistribute the land.
The first politicians also emerged on that period. The society of the time was ; the system of taxes and the clergy continued, and at the top of the hierarchy were those families that had the power during the Old Regime. In Gizaburuaga, the Bengoleas were the most powerful family. In , they became members of the Villarreal de Berriz family through marriage.