The findings deepen the mystery surrounding the cause of debilitating condition, also known as myalgic encephalomyelitis (ME).
Scientists dismissed previous claims that two viruses – XMRV and pMLV – may underlie CFS.
"We found no evidence of infection with XMRV and pMLV," said Dr Ian Lipkin, a member of the research team from Columbia University, New York City.
"These results refute any correlation between these agents and disease."
CFS is a serious physical illness that can cause severe tiredness, muscle weakness, aches and pains, memory loss, and poor sleep.