The effect of temperature and relative humidity (RH) on the time course of the rhythmic endogenous changes of chilling resistance was studied in cotton (Gossypium hirsutum L. cv. Deltapine 50) seedlings grown under light-dark cycles of 12:12 h. The resistant phase to 5° C, 85% RH lasted during most of the dark period while to 5° C, 100% RH it was longer and extended into the last half of the light period because a transient phase advance occurred when chilling started at the middle of the light period. Seedlings acclimated by low temperature were resistant throughout the light-dark cycle. A treatment with 100% RH before chilling to acclimated seedlings introduced a sensitive phase that corresponded to that of non-acclimated seedlings. In non-acclimated seedlings, this treatment decreased the resistance but the basic pattern of the rhythm was sustained. Changes in chilling resistance were analyzed under fluctuating temperatures and RHs, and explained taking into consideration the functioning of the circadian clock and environmental induction of resistance.