Cassava roots have a short shelf life due to a process known as post-harvest physiological deterioration (PPD). Within 2-3 d undesirable vascular streaking in the root develops. Tolerance to PPD was recently reported in different cassava genotypes, opening up new opportunities to analyze biochemical changes in stored roots and in the functional properties of their starches. Roots from PPD-susceptible (HMC-1) and tolerant (AM 206-5) clones were harvested and stored for up to 14 d in ambient tropical conditions. AM 206-5 is also characterized by amylose-free starch. Roots and starch were analyzed each day. PPD levels differed significantly between the two clones (35% and 8% at day 14) and showed a relation to scopoletin synthesis, which reached maximum levels around day 3 or 4 of storage. Roots lost weight consistently during storage (?10% in two weeks). Starch loss per day of root storage was estimated at about 1%. This could be the result of consistent increases in total sugars and respiration of root tissue. Important changes in starch properties were observed. Gel clarity decreased gradually during storage, with more pronounced changes occurring in starches from HMC-1. Swelling power decreased only in the case of AM 206-5. Gel viscosity increased in both genotypes. Improved tolerance to PPD could significantly reduce the economic impact of the short shelf life of ordinary cassava root processing. It remains to be seen, however, whether changes in stored roots positively or negatively affect the quality of the final product.