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Vahtre was born in Laiuse Parish (now Jõgeva Parish, Jõgeva County). He ended his studyings in University of Tartu in 1955 and worked there until 1993. He studied Estonian agrarian history, medieval chronicles, cultural history, Estonia's Christianization in the 13th century and St. George's Night Uprising. In 1973 he received a PhD. In 1989 Vahtre reestablished the chair of Estonian history University of Tartu and was its chairman until his retirement in 1993. Until his death in Tartu he was the most important historian in Estonia, the chief editor of the sequence of Estonian history (he edited volumes IV and VI) and also a book of Estonian Chronology (first edition 1994, second 2007).