High-throughput platforms for microalgae screening are not yet commercially available. In this study, the feasibility of 96-well microplates was analyzed for microalgae research. Equivalence among wells, as culture microreactors, was investigated in controlled high CO2 conditions. Specific growth rates of two microalgae species, Scenedesmus sp. UTEX1589 and an environmental isolate, were significantly higher in border wells than in internal positions. Furthermore, growth rate gradients analyzed as contours throughout the platform were observed for Scenedesmus sp. However, the output variable exhibited high precision associated with a low coefficient of variation (CV), between 6.8 and 7.8%. In a demonstrative experiment to determine the effect of culture media dilution on six microalgae species, treatments were randomized in the central subset of a microplate. Results were consistent and statistically sound (CV 9.4-12.9%), and showed that microalgae species could grow with no detrimental effect in 50% (v/v) dilution of the culture medium. Provided border wells exclusion and a randomized design, 96-well microplates are a practical and statistical robust platform for microalgae research. (c) 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:638-644, 2013