An integrated circuit may implement a masked substitution box that includes a counter that generates counter values. An input mask component may generate unmasked input values based on a combination of respective counter values and an input mask value. Furthermore, a substitution function component may receive the unmasked input values and may generate output values based on respective unmasked input values and a substitution function. An output mask component may generate masked output values based on a combination of respective output values and an output mask value. The masked output values may be stored at memory elements.