Aside from claims of irregularities, four blasts hit Karachi as people voted, killing 14 people and wounding dozens. Across the country, 29 people were killed in Election Day violence.
Despite pre-election attacks, voters lined up at dawn at polling stations nationwide, eager to send off the caretaker government put in place in March.
"This is the first time I am voting and I am 60; I want change," said Shaheen Khan, who was at a polling station in Karachi, the nation's largest city. "There were thousands of people when I came. ... The queue was so long, people in wheelchairs and crutches all waiting to vote."
Waits of three hours or more were reported at some polling stations. Election officials also reported delays in opening at some polls, the official Associated Press of Pakistan news agency reported.
A statement from the office of interim Prime Minister Mir Hazar Khan Khoso thanked the people of Pakistan for "coming out in huge numbers" to vote, as well as everyone involved in participating in and organizing the elections.
He voiced "confidence that the next phase of counting of votes will also be completed smoothly," and reiterated the determination of the caretaker government to hand over power to the winners without delay.
More vote-rigging claims
The leader of the governing Pakistan People's Party, Taj Haider, alleged vote rigging in some constituencies in Sindh province and its capital, Karachi, in a news conference broadcast by CNN affiliate Geo TV. Haider called on the country's Election Commission to hold a new vote in the affected constituencies.
Leaders of the Sindh-based Muttahida Quami Movement, one of Pakistan's largest and most liberal parties, told reporters that they would boycott the elections over allegations of rigging.
The Sunni Ittehad Council and Jamaat-e-Islami parties also announced a boycott, Geo TV reported.
Many Pakistanis hope the polls will usher in reform in a country battling issues including corruption, a struggling economy and security threats.
President Asif Ali Zardari condemned Saturday's election violence but said the militants' "cowardly acts" would not stop people from exercising their right to vote.
An open letter from Malala Yousafzai, the Pakistani schoolgirl who was attacked by the Taliban last year for her efforts to promote girls' education, urged everyone, and particularly women, to use their votes.
"If we want education, electricity and natural gas in our country, we must take a step," said her letter, published by Pakistan's Dawn website. "Let's vote for our country. We never realized how much powerful our vote is. One vote can change our country."
Blasts target voters
In some cities, the insecurity was evident Saturday.
Two of the blasts in Karachi targeted the Awami National Party office, killing 11 and wounding 36, said Naeem Shah, a spokesman for Karachi police.
A third explosion was in the Karachi suburb of Landhi. It killed three people and wounded nine, according to the deputy commissioner of Malir district, Qazi Jan Mohammed. Voting continued afterward, he said.
A fourth explosion, which wounded four people, was in the Peerabad area of Karachi, Shah said.
Fakhruddin Ebrahim, the chief election commissioner for Pakistan, said he contacted the military over security concerns in Karachi and the harassment of polling station staff in the city. He said polling material was stolen in several areas.