Mendoza said she was shocked by the allegations and, most of all, she hopes they're not true.
Mendoza is investigating whether the next city vehicle sticker depicts gang signs.
The sticker is meant to honor city firefighters, paramedics and police.
The sticker was designed by a 15-year-old boy who attends a school for troubled youth.
The clerk's office started getting phone calls Tuesday after an internet blogger identified the hands drawn on the sticker as symbols flashed by members of a street gang.
The stickers were about to be printed but that is now on hold.
Around 18,000 Chicagoans voted for the boy's design late last year in a contest.
When the boy won last month, he praised first responders, saying they have done a lot for him and his family.
According to the Chicago Sun-Times, the boy's facebook page shows him wearing a gang color and has photos of other young people flashing gang signs. ABC7 could not reach the boy's family for comment.
"You can imagine my surprise when these allegations surfaced today, but none the less, they have to be taken very seriously," Mendoza said. "We're doing our best to look into all the facts that surround this little controversy and hopefully put it to rest by making a decision that are based on the facts.
"I would never want to do anything that would give gang members the perception that they are supported in this city. The sticker is meant to do everything contrary to that. It is meant to honor police, fire, and paramedics."
Former police Supt. Jody Weis, now the president of the Chicago Crime Commission, said gangs "are the single biggest detriment to our society. We just can not have something that could, in the slightest way, reflect upon a particular game."
Mendoza is meeting with police as part of her investigation. She said there is time to change the design.