Prosecutors said Monday that a 16-year-old boy alerted state police to the abuse, which involved a variety of animals.
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On Saturday, police searched a property where the men live in Munson, Pennsylvania, 130 miles northeast of Pittsburgh, and seized recording equipment, cameras and homemade videos.
Clearfield County District Attorney William A. Shaw Jr., identified the men as Terry Wallace, 41, Matthew Brubaker, 32, and Marc Measnikoff, 34.
According to court documents, the teen claims that the men had sexual relations with dogs, horses, a cow and goat and that there was a designed "V" shaped pen that was used to facilitate the sexual contact.
The men are charged with child endangerment and corruption of minors as well as over 1,400 counts each of sexual intercourse with animals. They also were issued animal cruelty citations.
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The Centre Daily Times reports the men were jailed in lieu of $100,000 bond. Court records didn't list lawyers for them.
Shaw said that authorities and the SPCA in the area are in the process of finding a place for the animals to live.
Shaw also said that the 16-year-old was taken into protective custody but that there are no allegations that he had been sexually molested.
"Right now we don't believe the juvenile was sexually victimized," Shaw said.
He said that this was one of the most extreme cases of animal abuse that his office has handled.
The Associated Press contributed to this report.