The 1999 Meistriliiga was the ninth season of the Meistriliiga, Estonia's premier football league. Levadia won their first title.
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Lelle won 4âÂÂ2 on aggregate and retained their Meistriliiga spot; however, Lelle ceded their league entry to FC Valga both being associate clubs of Flora
Each team played every opponent four times, twice at home and twice on the road, for a total of 36 games.