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Sharing the same compact case design with three expansion slots, the IIci improved upon the IIcx's 16 MHz Motorola 68030 CPU and 68882 FPU, replacing them with 25 MHz versions of these chips.
The 40 MHz speed referred to the main logic board clock (the bus), the Motorola 68030 CPU, and the computer's Motorola 68882 FPU.