That could mean trouble for people who want to embark on long-term missions to Mars.
The data presented at an American College of Cardiology meeting in Washington was based on 12 astronauts who had ultrasounds while in space.
Their hearts grew 9.4 per cent more spherical in microgravity, and they also weakened.
"The heart doesn't work as hard in space, which can cause a loss of muscle mass," said James Thomas, lead scientist for ultrasound at NASA and senior author of the study.
"That can have serious consequences after the return to Earth, so we're looking into whether there are measures that can be taken to prevent or counteract that loss."
The astronauts' hearts returned to their normal, more oval shape, shortly after their return to Earth.
Astronauts currently spend up to six months at the orbiting International Space Station, which is staffed by rotating crews.
Missions to Mars, foreseen in the next couple of decades, would take about 18 months and may offer no return trip.