With more than 65%, Croatia was opposed to a change of its constitution to allow same-sex couples to marry and decided that marriage would be described as a union between a man and a woman.
Poland, Bulgaria, Latvia and Lithuania also prohibit marriage equality in their constitutions.
The European LGBT rights group, ILGA-Europe, said it is very disappointed by deputies who allowed this referendum (104 deputies out of 151 voted to allow it).
Gabi Calleja, co-chair of ILGA-Europe’s executive board, said: "We are seriously concerned by the fact that opponents to equality for all are using democratic tools to impose majority views on the rights of minority groups.
"We believe human rights and issues concerning minority groups cannot and should not be subjected to the popular vote in the first place.
"In a democracy, elected officials have a clear responsibility to safeguard human rights of everyone and not to allow democratic tools to be abused to restrict the rights of minority groups."