The voting underscored the deepening tensions in the strategic Gulf nation, a major oil producer and hub for US ground forces as part of the Pentagon's military counterweight to Iran.
Opposition groups - ranging from hardline Islamists to Western-leaning liberals - have already called the new parliament illegitimate because of the boycott and could increasingly shift their protests to the streets against Kuwait's ruling family.
The anti-government groups have bitterly denounced a decree in October by Kuwait's emir to end an unusual balloting system that allowed four choices per voter.
Critics claim the new one-vote-per-person rule will make it easier for state authorities to potentially influence the outcome. On the eve of the election, more than 15,000 people joined a peaceful pro-boycott march in the first rally permitted by authorities since a ruling last month banning gatherings of more than 20 people.
Security forces watched over polling stations, but there were no immediate indications of unrest or boycott supporters trying to disrupt the voting. Some opposition groups predict turnout could be well below 50 percent.
Kuwait has the Gulf's most political powerfully parliament, which was in the hands of Islamists and their allies earlier this year before the courts dissolved it over a legal challenge by the ruling establishment over electoral districts.
The country also has some of the widest political and media freedoms among the Gulf Arab states, but key government posts and policies remain under the control of the ruling family.
The region's popular uprisings have not spilled over to Kuwait in a major way as in nearby Bahrain, and it remains unlikely opposition groups would wage an all-out challenge to the current system and risk losing the generous cradle-to-grave benefits provided by the state.
But clashes last month between protesters and security forces displayed the potential for violence to escalate.
Kuwait also has been hit by a wave of labor unrest and strikes earlier this year, including walkouts that grounded the state carrier, Kuwait Airways, and temporarily closed customs posts and left several hundred trucks stranded at the border.
Calls for better working conditions have grown louder in the wake of the Arab Spring uprisings. Kuwaitis are used to well-paid government jobs and benefits that increasingly have become a burden on state finances despite the country's huge oil wealth.