One man aged 25 was killed after a tree fell on his car and another man, 65, died after he was trapped under a piece of roof that came loose from a building, reported Le Parisien.
A 92 -year-old man was also killed when his barn collapsed.
All in all firefighters were called out over 1,000 times as the storms cut off electricity and brought down trees.
The storms have been battering central France throughout the morning and afternoon, prompting France's weather agency to issue weather alerts for 26 départements.
These areas were placed on Orange alert – the second highest warning level – at 6am on Wednesday.
“A very turbulent and complex weather system is currently passing over the country,” said the country's weather service Météo France at the time.
The Auvergne region and the area around the city of Lyon will be particularly affected, forecasters say.
Hail storms and winds of up to 120 km/h were predicted.
There has also been torrential rain over the Cevennes region that are expected to continue until Thursday.
The départements with warnings in place for strong winds are as follows : L'Ain, la Drôme, l'Isère, le Rhône, la Saône-et-Loire et l'Ardèche
And those on alert for storms are : La Loire, la Haute-Loire, le Puy-de-Dôme, la Corrèze, la Creuse, la Haute-Vienne, la Charente, la Charente-Maritime, les Deux-Sèvres, la Vienne, l'Allier, l'Aube, le Cantal, le Cher, la Côte-d'Or, l'Indre, le Loiret, la Haute-Marne, la Nièvre et l'Yonne.
Violent storms across southern France at the weekend left a trail of destruction and a huge clean up operation had to be undertaken.
Click here to see more images from the damage.