Šiškauskas was a member of the senior men's Lithuanian national basketball teams that won the bronze medal at the 2000 Summer Olympics, and the bronze medal at the EuroBasket 2007. He was also a member of the Lithuanian team that won the gold medal at the EuroBasket 2003. He also played at the EuroBasket 2001, at the 2004 Summer Olympics, at the EuroBasket 2005, and at the 2008 Summer Olympics.