While there was no change to the S&P/ASX 20 or S&P/ASX 50, Atlas Iron and Lynas Corporation were removed from the S&P/ASX 100.
Atlas shares lost nearly 30% over the June quarter, while Lynas dropped around 25%.
Both remained in the S&P/ASX 200, while Discovery Metals and Mineral Deposits were removed.
Discovery was also removed from the S&P/ASX All Australian 200 along with Coalspur Mines, Mirabela Nickel and contractor Macmahon Holdings.
The biggest change was in the S&P/ASX 300, where ABM Resources, Ampella Mining, Bandanna Energy, Base Resources, Blackthorn Resources, Cape Lambert Resources, Cockatoo Coal, Focus Minerals, Flinders Mines, Grange Resources, Gryphon Minerals, Galaxy Resources, Hillgrove Resources, Inova Resources, Metminco, Northern Iron, Perilya, Red 5, Ramelius Resources and Rex Minerals were removed.
The changes are effective as of the close of trading on September 20.