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Although plant characterization under the International Potato Center’s (CIP’s) aeroponic system requires many morpho-physiological parameters to evaluate a cultivar, there is no method to evaluate the best parameters or the most suitable cultivation time. Thus, several morpho-physiological parameters were compared under a modified aeroponic system, using different statistical tools, to determine the best parameters and most efficient time to characterize seed-potato plants. We evaluated 21 parameters for cv. Agata under a randomized complete block design with weekly harvests for 9 weeks. The best parameters for growth characterization were selected based on multivariate statistical approaches involving correlation plots, similarity clusters (dendrograms), and principal component analysis. The best parameters for seed potato characterization were as follows, in order of importance: main stem diameter, leaf number, the length of the fourth leaf, leaf area, number of mini-tubers, mini-tuber fresh weight, root dry weight, and total dry weight. The days after transplanting (DAT) significantly affected the morpho-physiological parameters, with 45 DAT being the best cultivation time to estimate mini-tuber yield, and the data for bi-weekly harvests were as reliable as for weekly harvests. Our results, applied to either the CIP or to our modified aeroponics method, will be valuable in streamlining the characterization of other seed potato cultivars used by certified producers. Full article