Babtai were mentioned in 1394 in Die Littauischen Wegeberichte of crusaders as patrimony (kiemas Baptindorf).

Most likely the same place was mentioned in the report of Teutonic spies - "von dannen czu Bapto j mile" in 1386.

Situated on the historic road from Kaunas to Riga, it played a role in the trade between Lithuania and Livonia.

[1] At the turn of 1918 and 1919, the mostly Polish inhabitants of the Babtai commune sent a resolution to Kaunas, declaring that they would neither pay taxes nor recognize mobilization decreed by the Lithuanian government.

In response, the Lithuanian government sent troops to Babtai, which enforced compliance through arrests and penalties.