Nearly 100 women were involved in the study
The contraceptive pill could lead to women choosing the wrong partners, scientists believe.
Researchers found that women chose different partners after taking the pill in tests on nearly 100 women.
Women are thought to use smell to identify people with different immune systems and complementary genes.
But the joint Liverpool and Newcastle universities' study suggested the pill disrupted this process, the Proceedings of the Royal Society B journal said.
By passing on a wide-ranging set of immune system genes, couples increase their chances of having a healthy child that is not vulnerable to infection.
Partners with different genes are also less likely to experience fertility problems or miscarriages.
Women are naturally attracted to men with immune system genes different from their own because of their smell, experts believe.
The major histocompatability complex cluster of genes which helps build proteins involved in the body's immune response is also known to influence smell signals called pheromones.
It is this, experts believe, which leads women to use their sense of smell in helping to choose partners.
Researchers asked nearly 100 women to sniff six male body odour samples and say which one they preferred.
The test was carried out before and after the women had started taking the pill with very different results.
The researchers suspect that the results were related to the way the pill simulates a state of pregnancy in women.
Once pregnant, the need for a compatible partner for children recedes, they believe.
But lead researcher Dr Craig Roberts warned such changes could lead to problems.
"It could ultimately lead to the breakdown of relationships when women stop using the contraceptive pill, as odour perception plays a significant role in maintaining attraction to partners."