The elections were held to elect members of city councils, mayors, members of county councils and county prefects.
In Zagreb, populist right-wing and former Social Democrat Milan Bandić won 47.9% of the vote against Social Democrat Health Minister Rajko Ostojić's 22.7%.
Bandic received a two-thirds majority in the second round.
The incumbent mayor of Split, Željko Kerum, placed third with 18.54% of the vote and was eliminated from the second round which was narrowly won by the Socialist candidate Ivo Baldasar.
In Slavonia's largest city, Osijek, the HDSSB candidate, mayor Krešimir Bubalo, won 36.3% of the vote in the first round, but lost to Independent candidate Ivan Vrkić, who gained 27.8% in the second round.