In the second half of the 16th century, the area is colonized by Croats who flee their homes before the Turks advance. The important historian of Hungary Gabriel Kolinovič Šenkvický wrote, based on the data of historians J. Sdegedy and S. Timon , that Šenkvice was founded by Croats between 1544 and 1550. Croatian colonists from Kostajnice and the surrounding area were brought to Šenkvíc by Mikuláš Šubič at the time when the Turks destroyed Kostajnica. In 1594 , other Croatian refugees came, founding a new settlement near the existing settlement near the Sisek stream, which Count Štefan Ilešhazi called Malé Šenkvice, originally named Sisek.
From 1647 the village belonged to the Pálffy family (Pezinok estate).
The surroundings of Šenkvíce were inhabited as early as the Neolithic, and there are finds from the Early Bronze Age as well as from Roman times. The first written mention of the village is from 1256 in a document of the Hungarian king Bela IV. After the Tartar invasion and plunder of Hungary, German colonists came to the territory of the Pezinok estate. The first Germanized name known from the document of the vicar of the Archbishop of Esztergom, Leonardo de Pansauro, dates from 1390, where the parishes of the Bratislava post office are named. Among them is Šenkvice SAMKAWYCH, listed between Modra and Vistuk.