The study has been done by Leah Lakdawala of Michigan State University and Prashant Bharadwaj of the University of California, San Diego in USA.
The study clearly says sex discrimination begins in the womb in male-dominated societies such as India.
"It paints a pretty dire picture of what's happening," said Lakdawala, MSU Assistant Professor of Economics.
The study says although it is illegal for a doctor to reveal the sex of an unborn baby or for a woman to have an abortion based on the baby's sex in India, but the mal-practises are rampant in the country.
However, knowing the sex of the baby through an ultra-sound also can lead to discrimination for those pregnancies that go full-term, she said in a statement.
In studying the national health-survey data of more than 30,000 Indians, the researchers found that women pregnant with boys were more likely to go to prenatal medical appointments, take iron supplements, deliver the baby in a health-care facility - as opposed to in the home - and receive tetanus shots.
Tetanus is the leading cause of neo-natal deaths in India.
According to the study, children whose mothers had not received a tetanus vaccination were more likely to be born underweight or die shortly after birth.
The researchers - the first to study sex discrimination in prenatal care - also looked at smaller data sets from other countries.
In other patriarchal nations of China, Bangladesh and Pakistan, evidence of sex-discrimination in the womb existed.
But in Sri Lanka, Thailand and Ghana - which are not considered male-dominated - no such evidence existed.
"This type of discrimination we're seeing, while not as severe as sex-selective abortion, is very important for children's health and well-being," Lakdawala said.
Given that previous research has linked early childhood health to later outcomes, sex discrimination in pre-natal care might also have long-term effects.
"We know that children born at higher birth weights go to school for longer periods and have higher wages as adults, so the future implications here are pretty serious," Lakdawala said.