Some alterations lasted at least two years, they reported, but did not appear to erode memory or other mental processes.
The changes "concern brain areas associated with functions necessary to manage the challenges of motherhood," study co-author Erika Barba-Muller of the Autonomous University of Barcelona (UAB) said in a statement.
The radical hormone surges and physical changes of pregnancy have long been known and studied, but its effects on the brain have been little understood.
The new study, published in Nature Neuroscience, claims to provide the first evidence "that pregnancy confers long-lasting changes in a woman's brain."
It compared pre- and post-pregnancy brain scans of 25 first-time mothers. They researchers also looked at the brains of first-time fathers, as well as men and women with no children.
It found "pronounced and long-lasting GM (grey matter) volume reductions in a woman's brain" in pregnancy, in regions involved in social processes.
In later tests, these same regions lit up most on scans measuring the women's responses to their babies.
The brain changes were likely an adaptation for motherhood — boosting the ability to recognise the needs and emotional state of a baby and decode potential threats to its health and safety, said the researchers.
Grey matter is found in the brain's wrinkly outer layer called the cerebral cortex, which houses the processes of learning and memory, motor function, social skills, language and problem solving.
The good news: the researchers "did not observe any changes in memory or other cognitive functions during the pregnancies and therefore believe that the loss of grey matter does not imply any cognitive defects," said a UAB statement.
The study tested the women up to two years after pregnancy, so it is not clear how long the changes last.
The study pointed to a process called "synaptic pruning" which happens to humans in adolescence to remove rarely-used synapses — connections between brain cells.
This is done to make way, after childhood, for more efficient and specialised synapses and boost the network's overall efficiency.
A similar process may be at play in pregnancy, the researchers speculated.