In 1933, Prelog married Kamila Vitek. The couple had a son Jan (born 1949).
An intellectual with a wide cultural background, Prelog was one of the 109 Nobel Prize winners who signed the peace appeal for Croatia in 1991.
Vladimir Prelog died in Zürich, at the age of 91. An urn containing Prelog's ashes was ceremoniously interred at the Mirogoj cemetery in Zagreb on 27 September 2001. In 2008, a memorial to Prelog was unveiled in Prague.