Simultaneous exposure of Au and In2O3/SnO2 (ITO) electrodes to an equimolar solution of a thiol and a carboxylic acid or a thiol and phosphonic acid results in the selective attachment of the thiol to the Au electrode and the carboxylic or phosphonic acid to the ITO electrode. This selective surface-attachment chemistry is termed "orthogonal self-assembly" (OSA) and can be used to direct the spontaneous assembly of molecular reagents onto Au and ITO microstructures. The selectivity of the thiols for Au and the carboxylic or phosphonic acids for ITO:is determined by a combination of cyclic voltammetry experiments using ferrocene-tagged molecules, scanning Auger microscopy, and imaging secondary ion mass spectrometry (SIMS) to map the distribution of thiols, carboxylic acids, and phosphonic acids on derivatized Au and ITO microstructures.