Bagatskis, a long-time national team player who is now coaching Russian club Enisey Krasnoyarsk, has been given a two-year contract.
The 42-year-old will guide Latvia against Israel, Finland, Montenegro and Italy in EuroBasket 2011 qualifying this summer.
Bagatskis will bring in former Latvia teammate Roberts Stelmahers as his main assistant.
Stelmahers is currently at the helm of Lithuania club Perlas Vilnius.
Latvia had high hopes going into EuroBasket 2009 in Poland under Lithuanian coach Kestutis Kemzura but failed to progress from their Preliminary Round group after win one in their three games.
The Baltic country offered Kemzura a chance to continue in the job but he declined and was later appointed coach of Lithuania.
Bagatskis played at four EuroBaskets – the last in 2003 in Sweden.