Background: Microplate-based immunoassays are widely used in clinical and research settings to measure a broad range of biomarkers present in complex matrices. Assay variability within and between microplates can give rise to false-negative and false-positive results leading to incorrect conclusions. To date, the contribution of microplates to this variability remains poorly characterized and described. This study provides new insights into variability in immunoassays attributable to surface characteristics of commercial microplates. Methods: Well-to-well assay variation in γ-treated and nontreated 96-well opaque microplates suitable for chemiluminescence assays was determined by use of a validated sandwich ELISA. Microplate surface characteristics were assessed by sessile drop contact angle measurements, scanning electron microscopy, energy dispersive x-ray spectroscopy, and atomic force microscopy. Results: All microplate types tested exhibited vendor-specific assay response profiles; and "rogue" plates with very high intraassay variation and deviant mean assay responses were found. Within-plate, location-dependent bias in assay responses and variability in well contact angle were also observed. We demonstrate substantial differences in well-surface properties with putative effects on protein-coating reproducibility and hence consistency in immunoassay responses. A surface "cleaning" effect on manufacturing residues was attributed to γirradiation, and treated microplates manifest increased polar functionalities, surface roughness, and assay responses. Conclusions: Our data suggest that tighter control of variability in surface roughness, wettability, chemistry, and level of residual contaminants during microplate preparation is warranted to improve consistency of ELISA assay read out. IMPACT STATEMENT In clinical and research settings, microplate-based immunoassays are subject to assay variability within and between microplates that can give rise to false-negative and false-positive results leading to incorrect conclusions. This article clarifies the contribution of microplates to assay variability, which is poorly understood to date. Detailed physicochemical analyses of microplate well surfaces provided new insights into immunoassay variability attributable to microplate surface properties and preparation processes. Our work prompts further investigations to elucidate surface parameters that influence antibody adsorption and biofunctionality, highlighting manufacturing issues that require further review to overcome problems with microplate variability and assay performance.