The DuPage County Board rejected a requested height variance that would have allowed the construction of a minaret and dome for the mosque.
Board members say the structures were too large for the neighborhood.
The minaret was measured at 79 feet and the dome at 69 feet.
The Muslim Educational Cultural Center of America is planning to build the estimated $14 million project at 91 St. and Kingery.
Existing zoning law limits structures to 36 feet in height.