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Head-starting of Agassiz’s desert tortoise, a means to aid recovery of this threatened species, may adversely affect offspring sex ratios via temperature-dependent sex determination combined with possible unnatural thermal conditions in head-start facilities. We determined sex ratios in juvenile tortoises hatched from first clutches of 4 annual cohorts at the head-start facility at the US Marine Corps Base, Twentynine Palms, California, USA, using non-fatal, endoscopic inspection of gonads. Cohort sexes ranged from 97% females (female:male ratio of 6.25:1) in 2008 to 84% males (female:male ratio of 0.19:1) in 2009, apparently primarily in response to local weather conditions during the temperature-sensitive phase of incubation. Warmer weather during development of a second clutch laid in 2009 led to fewer males (55%, female:male ratio of 0.82). Efforts to cool (artificially shade) some nesting burrows were unsuccessful in increasing the proportion of male hatchlings in 2009. Cohort sex ratios were associated with average daily air temperatures during incubation, such that more females were produced during warmer periods, in good agreement with published temperature-controlled laboratory experiments. These results suggest that weather played a major role in determining sex ratios, with apparently smaller or negligible influences resulting from initial location, structure and operation of the head-start facility; experimental shading of nests; and individual mothers’ variation in the timing of egg laying and placement of nests within the natal burrows. These results, obtained from a remote, mostly natural field site, indicate the potentially great sensitivity of sex determination in nests of wild, free-living desert tortoises to changes in climate.