Mark Hammond said bias against pregnant women or those returning to work after maternity leave "needs to be tackled".
Launching a new EHRC research project, Mr Hammond vowed to uncover the extent of the problem.
Anecdotal evidence suggests that some pregnant women experience prejudice while on maternity leave or on their return to work, an ECHR spokesman said.
The review will examine pregnancy and maternity discrimination in the workplace.
Experts will investigate employers' practices towards workers who are pregnant or on maternity leave, and these employees' experiences.
Mr Hammond said: "It is very concerning that in 2013 a number of women are still being disadvantaged in the workplace just because they are pregnant.
"That would be unlawful discrimination and needs to be tackled.
"We will look at existing research, gather new evidence and carry out our expert analysis to establish the extent of the problem and advise on how best it can to be addressed."
"The principles of non-discrimination were established decades ago and should be accepted as an essential part of the business environment.
"Since the economic downturn began, pregnant women and new mothers have faced an increasingly difficult time in the workplace. Unfair and unlawful treatment of new mothers is widespread and action is urgently needed.
"Pregnancy discrimination imposes major costs on new families at a time when they are least able to handle additional financial stress."
Employment lawyer Kiran Daurka, of Slater & Gordon, said: "Mothers - whether expecting children or returning to work - are a vital part of Britain's workforce. We need to treat them better.
"We are delighted to hear that the EHRC is to undertake some very important and much needed work around maternity discrimination.
"Following our own findings over the summer, which revealed that more than a quarter of mothers feel discriminated against, it is clear that urgent action is needed to protect pregnant employees and those returning from maternity leave."
Gloria De Piero MP, Labour's shadow minister for Women and Equalities, said: "Labour has been calling on the Government for months to properly investigate the extent of pregnancy discrimination, so this is welcome news.
"It is shocking that three years after Labour made pregnancy discrimination illegal, so many women are still losing their jobs or finding they have been sidelined after taking maternity leave.
"But Maria Miller needs to wake up to the impact of her own Government's policies. Low paid new mums have lost almost £3,000 in support in the first two years of their baby's life under this Government, and by introducing £1,200 tribunal fees costing the equivalent of nine weeks maternity pay, challenging maternity discrimination has increasingly become unaffordable for new parents struggling with the rising cost of living.
"Labour will strengthen the law to grant greater protection for new mums against discrimination and raise the responsibility on employers to take positive steps to support new mums who want to return to work."