We investigated associations between rainfall and body condition of desert mule deer (Odocoileus hemionus eremicus) in the Sonoran Desert, California, using two indices of condition based on body fat: a categorical score based on subcutaneous fat and visibility of bones under the skin of free-ranging animals via remote photography, and percent fat in the marrow of long-bones of harvested males. There were positive correlations between rainfall and proportion of deer in good condition (r  =  0.60, P  =  0.064) and proportion of deer in fair condition (r  =  0.70, P  =  0.017). Proportion of deer in poor condition was negatively correlated with rainfall (r  =  −0.72, P  =  0.020). There was evidence of a year effect on percent fat in the marrow of metacarpus and metatarsus bones (P  =  0.030), such that years in which deer had lower average marrow fat coincided with years having lower rainfall. These findings demonstrate the importance of rainfall, likely operating through quantity or quality of forage, on body condition of mule deer, which have subsequent effects on demography. An understanding of these patterns will continue to be important for the conservation of ungulate populations in arid regions.