Neither of the two men's names have been released yet and it is unclear if they were Amazon employees or third-party contractors.
News reports cite Baltimore fire officials as saying one man was found under debris Friday night and later pronounced dead, while a second man's body was recovered under rubble early Saturday. No other injuries were reported.
"First responders remain onsite assessing the damage".
A 50-by-50-foot wall collapsed at the facility, which is located in southeast Baltimore, at around 10:30 p.m. on Friday.
The site was still an active scene as of Saturday afternoon, and an Amazon spokesperson told the paper that the building had been closed.
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'We are incredibly thankful for the quick response from emergency services. "Our thoughts and prayers go out to those impacted by yesterday's tragic event".
Storm damage at an Amazon Fulfillment complex in Baltimore. "The whole side (of the building) was just dropping", he said.
The National Weather Service reports the tornado Friday night packed winds peaking at around 105 mph (169 kph) and traveled 2.5 miles (4 kilometers) through Baltimore.
An Amazon official says the two people killed after part of a distribution warehouse in Baltimore collapsed amid severe weather weren't employees of the online retail giant, but worked for an outside company.