DNA microarrays have received considerable attention in the fields of bio- and nanotechnology due to their importance in the development of biosensing and diagnostic devices. The construction of these surfaces often entails the attachment of presynthesized oligonucleotides onto a derivatized surface. The hybridization efficiency of DNA microarrays and biosensors is determined in part by variables such as the density and orientation of the single stranded DNA oligomers used to build the devices. Surface analysis techniques such as X-ray photoelectron spectroscopy (XPS), near edge X-ray adsorption fine structure, time-of-flight secondary ion mass spectrometry (ToF-SIMS), and surface plasmon resonance (SPR) can aid in producing reliable, quantitative, and reproducible microarray chemistry. Our initial studies have used model surfaces of self assembled monolayers of thiolated DNA on gold to compare surface characterization (XPS and NEXAFS) of the DNA with hybridization efficiency (SPR and radio-labeling). Factors such as the DNA purity, DNA-surface interaction, and the non-fouling capabilities of the background are discussed. Commercial surfaces and surfaces modeled to simulate the commercial substrates are analyzed with surface analysis techniques as well.