The man, identified only as a 39-year-old living in Hudiksvall in central Sweden, had over five years caught and released thousands of birds but also kept some in cages, said the head of Sweden's ornithological association.
"We're talking about treatment of birds that was most definitely unfortunate," Dennis Kraft told AFP. "The birds were imprisoned only for the sake of his own pleasure and moreover under very bad conditions," he said.
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They were discovered last June following an anonymous tip to regional authorities.
When officials arrived at his house, they found about 500 birds dead and alive, Swedish public radio (SR) reported.
"It was a shock every time we opened a door. It smelled like ammonia, a lot of faeces and feed together with dead birds that were rotting," Gaevleborg county predator control specialist Daniel Hansson told SR.
The prosecutor for environmental crimes, Christer Jarlaas, told news agency TT the man had admitted to trapping the birds.
He had been charged with aggravated hunting violations and aggravated crimes against protected species and animal cruelty, which could land him between two and three years in jail, the prosecutor said.
"The man has said it started with both an interest in collecting things and some kind of desire to take care of injured birds and then release them, but then it spun out of control," he said.
Authorities found a computer in his home containing detailed descriptions of all the birds he caught, as well as nets and other material.

