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There is concern about how climate change might affect Agassiz’s desert tortoise Gopherus agassizii, a threatened species. We studied the effects of climatic variation on clutch phenology of a population at a wind energy generation facility for 7 field seasons between 1997 and 2011. Using X-radiography, we quantified the following phenophases based on the number of calendar days to each event from 1 January: appearance and disappearance of 65 first and 53 second clutches, and inter-clutch intervals between first and second clutches. Although third clutches were rare (n = 8), they were observed in 5 of 7 yr and were produced by 8 different females, all of which produced a third clutch only once during the study. Shelled eggs were visible from as early as 11 April to as late as 28 July, and the overall time span that eggs were visible differed among years. After controlling for maternal effects, we observed statistically significant inter-annual variation in all phenophases except for inter-clutch interval. Clutch appearance was late in cool years relative to warm years and especially late after 2 consecutive cool years. Using degree day (DD) methodology, we calculated DD accumulation during the post-hibernation and nesting season for each year. We then used DD estimates for mean date of first clutch appearance to predict the mean date of first clutch appearance in subsequent years with 1 to 10 d accuracy for all but 1 yr (1998) with El Nino conditions. Clutch phenology appears to be correlated with inter-annual variation in climate and may be influenced by climatic events in previous years.