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Manganese (Mn)-doped silicon nanocrystals (Si NCs) in which Mn is in its most likely substitutional or interstitial location have been investigated. Large differences in magnetic moment are found between Si NCs doped with substitutional Mn and those doped with interstitial Mn. For all the doped Si NCs, quantum confinement affects the electronic states of majority spin more significantly than those of minority spin. As the NC size changes from 1.2 to 1.5 nm, the spin flipping of electronic transition across the NC optical gap occurs for Si NCs doped with substitutional Mn. This leads to significant changes in the optical absorption of Si NCs. It is likely that such spin-flipping also happens for larger (>1.7 nm) Si NCs doped with interstitial Mn. [ABSTRACT FROM AUTHOR]