The election was originally scheduled for January 8 but the assassination of former prime minister Benazir Bhutto after a rally in Rawalpindi on December 27 forced a delay.
Polls opened at 8 a.m. (3 a.m. British time) and will close at 5 p.m. (12 p.m. British time). Results are expected to start emerging by midnight and trends should be clear on Tuesday morning.
The death of Bhutto, the most progressive, Western-friendly politician in a Muslim nation rife with anti-American sentiment, raised concern about stability in the nuclear-armed state. Well over 450 people have died in militant-related violence so far this year.
Voting got off to a slow start. Monday has been declared a holiday with financial markets and schools closed, and traffic was very thin on roads in cities across the country.
A woman voter, Azra Khalid Shaikh, heading into a polling station in the city of Karachi, said she wanted to set the country back on a path to democracy: "This is the starting point."
Former army chief Musharraf's popularity plunged over the past year because of his manoeuvres to hold on to power which included purging the judiciary and six weeks of emergency rule.
Many Pakistanis also blame the government for rising prices, shortages of staples and all too frequent power cuts.
Security concerns affect large parts of Pakistan, where Musharraf has ruled since seizing power in a 1999 coup, and a suicide attack on Bhutto party supporters killed 47 people in a northwestern town on Saturday.
"You see suicide bombings everywhere and you can see the empty streets on polling day. It's all because of fear," said civil servant Mohammad Ijaz who was voting in the city of Lahore where three people were killed in shootings late on Sunday.
A supporter of the opposition party led by former prime minister Nawaz Sharif was shot dead in Punjab province after polls opened, police said.
Militants set off bombs at four polling stations in the northwest, three in the Swat Valley, before polls opened but no one was hurt. Army gunship helicopters later attacked suspected militant hideouts in Swat, residents said.
