The purpose of this study was to investigate whether the effects of cooling and reheating on the glycaemic index (GI) of novel potato clones (selections) differed depending on selection and whether cooling altered starch absorption in vivo. We conducted 3 experiments using 4 novel potato clones in healthy subjects. Experiment 1: the GI of 4 selections each prepared in 3 ways (freshly boiled, cooled, or cooled and reheated) was measured in 2 groups of 10 subjects (each group tested 2 selections). Experiment 2 (n = 10): two selections from Experiment 1 were re-tested one year later, by a different subject group. Experiment 3 (n = 10): two selections from Experiment 1 were tested by subjects from Experiment 2 to assess the rate and extent of starch absorption using the second-meal effect and the breath hydrogen method, respectively. Experiment 1 demonstrated a selection×treatment interaction for GI (p = 0.024); cooling reduced the GI of two selections by 40–50% (p < 0.05) but reduced GI of the other 2 by only 8–10% (ns). Experiment 2 confirmed the selection×treatment interaction (p = 0.018) seen in Experiment 1. Experiment 3: cooling reduced the GI by an average of 37% (p < 0.05) but only increased starch malabsorption in vivo from 3% to 5% (p = 0.021); there was no significant second-meal effect. It is concluded that the effect of cooling on the GI of potatoes may vary from 0–50% depending on selection. However, the mechanism for the effect is not clear: the 2% increase in starch malabsorption seen upon cooling potatoes was not nearly enough to account for the 37% reduction in GI.