A high-throughput method has been developed to measure drug-cyclodextrin binding constants. It measures the distribution ratio of a drug between a polymer film [polyvinyl chloride (PVC) with 67% (w/w) dioctyl sebacate (DOS)] and a cyclodextrin-containing buffer in a 96-well format. Measurements of distribution ratios at several cyclodextrin concentrations lead to binding constants. Binding constants for econazole with six CDs have been determined in one 96-well microplate with four replications of each condition in 10 h. The K1:1/103 M−1 values are 3.98±0.13, 3.90±0.22, 29.3±2.2, 0.66±0.04 1.78±0.30, 4.08±0.50, with (2-hydroxyethyl)-β-cyclodextrin, (2-hydroxypropyl)-β-cyclodextrin, 2,6-di-O-methyl-β-cyclodextrin, hepta-kis(2,3,6-tri-O-methyl)-β-cyclodextrin, α-cyclodextrin, β-cyclodextrin, respectively. It is likely that 1:2 complexes are also formed in some cases. This method has also been applied to study the binding behavior as a function of the drug concentration and pH. Binding weakens at higher drug concentration which may be due to the self-association of the drug. An acidic environment decreases the binding constant of CD with the basic econazole. The formation of the 1:2 complexes is completely suppressed in acid as well. This protocol is faster than the phase-solubility method. Moreover, the material requirement is up to four orders of magnitude lower.