According to police, officers raided the home conducting a search warrant around 9:38 p.m. in the 4000-block of North Troy Street and found the reptile along with guns and drugs.
A spokesman for the police department declined to say what the search warrant was for.
The alligator was turned over to animal control, police said.
Richard Hallinan lives on the first floor and said he heard armed undercover officers break through the door.
"As I was listening, I heard broken glass and doors coming through," Hallinan said. "I got up grabbed my cell phone ran to the back of the house."
Gaby Salazar lives down the block and got a glimpse of the reptile as animal control took it away in a crate.
"This neighborhood is like really calm and nothing like that ever happens, so something like this yesterday, it was kind of intense for me," Salazar said.
Deborah Stewart is a volunteer with animal rescue shelter Famous Fido, just down the street.
"I don't know why they would keep something like that," Steward said. "They probably don't have any idea what to do to take care of it."
Hallinan said he never suspected any illegal activity from his two upstairs neighbors.
"They've been here for three years," Hallinan said. "I've been here for 15 and they were very polite and decent with me."
Hallinan said the men are in their 40s. Police told him they were not at home at the time of the raid.
No one is in custody. No further details about the investigation were immediately available.
Alligators in Chicago|
Last month, an alligator nicknamed "Chance the Snapper" was caught after days of evading trappers in the Humboldt Park Lagoon.
A few weeks later, two men claimed they fished another alligator out of the Humboldt Park lagoon in a Facebook Live video but police found "inconsistencies" in the story.