Stones missed England training on Wednesday with the Manchester City defender struggling badly with illness before the Three Lions kick-off in Germany.
There was an injury concern over the centre-back when he took a knock in the friendly with Iceland last week, but he was in training on Tuesday in Germany and all seemed well.
However, Stones has come down with illness since then and was not involved with the rest of the squad on Wednesday, causing concern ahead of the opener against Serbia on Sunday evening.
According to Sky Sports' Rob Dorsett, Stones was confined to his bedroom and effectively quarantined, to prevent the sickness bug from spreading to the rest of Southgate's party.
It has since emerged from The Telegraph that Stones has become a major doubt for the clash against Serbia - although the Football Association haven't confirmed the nature of his illness - and it remains unclear if he'll train on Thursday.
The other 25 players in the squad were training on Wednesday, with further encouraging signs for Luke Shaw, who is pushing for a return from injury.
The former Southampton man appears to be progressing well, though, and he looks set to feature in the group stages as he nears fitness again after the muscle problem.
The severity of Stones' illness is yet to be confirmed, but Southgate will be very keen to have him available on Sunday after Harry Maguire missed out on the squad through injury.
If Stone were not available then England would be lacking international experience at centre-back after Maguire's injury.
More Trending 
Euro 2024 sweepstake kit: Download your free printable pack
Jude Bellingham is also back with the squad after his extended break following Real Madrid's Champions League glory at Wembley.
For more stories like this, check our sport page.
Follow Metro Sport for the latest news on Facebook, Twitter and Instagram.
MORE : Liverpool launch inquiry for Stuttgart star Waldemar Anton
MORE : Pat Nevin urges Manchester United star to leave club after Euro 2024
MORE : Paul Scholes says England have made 'big mistake' leaving duo out of Euro 2024 squad