The four-year-old was left lying on folded towels in pain for five hours after suffering severe gastro.
It's the latest in a string of similar incidents.
In March, a 93-year-old man went 23 hours without a pillow or blanket at the Queen Elizabeth Hospital, and there was a similar issue at the Royal Adelaide.
The South Australian government recently launched a statewide pillow audit.
It found "sufficient stock" at the QEH and the Women's and Children's Hospital.
SA Health insists that remains the case but apologised to the boy's family.
Health Minister Chris Pickton says he personally went to the Women's and Children's to check on the pillow supply today.
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