Authorities say that rescue crews found the three men unconscious and unable to escape from the pit at the farm in Ohio.
Officials believe they were working to fix a manure pump when they passed out from the fumes, said St Henry fire chief MattLefeld.
The three men have been named as Gary Wuebker, 37; Brad Wuebker, 35, and Todd Wuebker, 31.
All three victims were taken to hospitals in the area where they were pronounced dead.
Manure pits are used on livestock farms to store waste before it is used as fertilizer on fields.
But the pits themselves can produce hazardous gases, such as hydrogen sulfide, methane, carbon monoxide and ammonia.
And some of those gases can lead to headaches, dizziness, breathing trouble and deaths, according to the Ohio State University Extension
The brothers all worked alongside their father at GBT Wuebker Farms, LLC.
A number of local farmers expressed condolences for the Wuebker family on social media after news of the tragedy.
“Our hearts are with the Wuebker Family,” wrote one fo the farms, Mercer Landmark, Inc.
“Brad, Gary and Todd Wuebker lost their lives doing what they loved - working on the family farm. Brad and Gary were members of our team and had a work ethic like no other.”
The Ohio Holstein Associationï»¿ said in a Facebook post, that their “condolences go out to the Wuebker family on the loss of their three sons, Brad, Todd, and Gary Wuebker of Mercer County.”
The Associated Press contributed to this report.