Ethnic Serbs were being encouraged to vote for the first time since the secession, which Belgrade has bitterly opposed but which is at the heart of an EU-brokered normalization deal struck earlier this year.
The day was marred by an attack on a polling station, along with the theft and destruction of ballot boxes, in the Serb-dominated section of the ethnically divided city of Mitrovice.
Masked men ransacked the main polling station there near the end of voting, reportedly throwing tear-gas canisters into the facility before smashing and stealing ballot boxes.
Voting at several other northern Mitrovica polling stations was halted as electoral officials and monitors from the Organization for Security and Cooperation in Europe (OSCE) were evacuated.
Election officials later appealed to the OSCE to help transport salvaged ballot boxes to a central counting station near Pristina.
The OSCE had no immediate comment on how the violence would affect the election or how ballot boxes from northern Kosovo would be transferred further south.
Domestic and international officials were following the turnout figure for ethnic Serbs, especially in the north, where they make majority and have so far defied Pristina's authority.
Up until around 3:00 p.m. local time, voter turnout in northern Kosovo’s municipalities ranged from 7 percent to about 13 percent.
Across the rest of Kosovo, official turnout for the day was said to have been 45.79 percent.
Soon after polling stations opened in the morning, reports emerged of problems.
Central Election Commission head Valdete Daka told RFE/RL’s Kosovo Unit hours into the voting that "certain groups in the northern part of the country are not allowing the citizens to freely express their will by voting."
"For this situation, Kosovo police and relevant institutions have been informed," Daka said. "We will also inform the European Union and the OSCE mission, although the OSCE must have been informed, since it has its personnel in the north."
Mitrovica mayoral candidate Krstimir Pantic -- a member of the Belgrade-backed civic initiative Srpske -- told journalists that he was prevented from casting a ballot and questioned the thoroughness of OSCE oversight.
"As things stand now, I was not able to cast my vote," Pantic said. "At this polling station, there are only two members of the Election Commission. According to the election law, at least three members have to be present at a polling station. What especially surprised me was that not even one representative from the OSCE was present. This has put in doubt the sincerity [of their claims] that the process would pass in a democratic and normal atmosphere.""
There are some 120,000 ethnic Serbs in Kosovo. The 40,000 living in the northern part of the country were concerned that if they voted, it would legitimize the state of Kosovo.
WATCH: Natural sound video from RFE/RL's Balkan Service of voting in the northern, mostly ethnically Serb, section of the divided city of Mitrovica:
Serbian President Tomislav Nikolic, Prime Minister Ivica Dacic, and Deputy Prime Minister Aleksandar Vucic had issued a joint statement saying that "only a high turnout will secure the Serbs' survival in Kosovo."
But Serb hard-liners in northern Kosovo were campaigning for a boycott.
Dragica Cerich, a resident of Mitrovica, said on election day that some local people had received "threatening messages."
"We voted today so that tomorrow becomes better. At least we hope so," Cerich told RFE/RL's Kosovo unit. "We listened to our [Serbian] President [Tomislav Nikolic], and [Serbian Deputy Prime Minister Aleksandar] Vucic. I voted because I have nothing. We received threatening messages over the phone, and this is what pushed me to go out and vote; this is shameful. I felt intimidated when going out to vote. They waited for us and threatened. I hope it will get better. Hope is always the last to die."
On the eve of the vote, Kosovar President Atifete Jahjaga told AP that the participation of Serbs would further integration.
Serbia, with Russian support, still officially rejects Kosovo's independence, unilaterally declared in 2008 by the ethnic Albanian majority.
Serbia was encouraging ethnic Serbs to vote as part of the normalization agreement that officials from the European Union helped Belgrade strike with Pristina.
That agreement in April 2013 has helped Serbia secure the green light to begin membership talks with Brussels.
Ahead of voting, EU foreign policy chief Catherine Ashton called on people throughout Kosovo to participate in the elections. In a statement, she described the vote as "a key moment in Kosovo's future and an important element in the process of normalisation of relations between Kosovo and Serbia."
"Changes, I expect positive changes," Agron Bajrami, a Kosovar Albanian lawyer in his 50s, told RFE/RL in the capital on election day. "Pristina is [in] chaos from the planning point of view. That chaos continues, so I sincerely hope for this situation to improve. I am aware that these are local elections and major changes cannot be expected, but there can certainly be changes on the local level. Municipal authority has been decentralized -- they run their own budgets -- and thus they should be able to invest public money instead of embezzling it."
About 1.7 million people across Kosovo were eligible to vote.
Prime Minister Hashim Thaci’s Democratic Party of Kosovo (PDK) was expected to win most of the ethnic Albanian votes.
WATCH: RFE/RL's Kosovo Unit director Arbana Vidishiqi discusses the significance of the vote: