Yahya al-Mahjari, a rights activist in Aden said that three youth from the southern movement were injured when security forces hit them with batons.
He said that clashes were lower than expected, but very few were heading to ballot stations to vote for soon to be president Abdurabu Hadi.
Election observers said that the turnout in the presidential elections was low but say that was expected.
In Mansoora district of Aden security forces shot live bullets to the air to disperse protesters who were burning tires and threatening those who were on their way to vote.
At least 20 percent of the polling stations were shut down in Aden by local officials after fearing that violence could erupt in certain districts.
Southern Movement protesters marched the streets of Aden and some tried to close down polling centers, a local council official in Mualla, Aden, said.
Yemen security officials are spread in numerous areas in Aden to ensure complete security during the election period.