Cidea and Cidec play an important role in regulating triglyceride storage in liver and adipose tissue. It is not known if the Cidea and Cidec genes respond to a high fat diet (HFD) or exercise training, two interventions that alter lipid storage. The purpose of the present study was to determine the effect of a HFD and voluntary wheel running (WR) on Cidea and Cidec mRNA expression in liver, adipose tissue, and skeletal muscle of mice. A HFD promoted a significant increase in Cidea mRNA in adipose tissue and liver, but not in skeletal muscle. The increase in Cidea mRNA in adipose tissue and liver was prevented by WR. Unlike adipose tissue and liver, WR resulted in a significant increase in Cidea mRNA in skeletal muscle of mice fed a HFD. Cidec mRNA increased in response to a HFD in all tissues, a process that was prevented by WR. Epididymal white adipose tissue (EWAT) mass was significantly related (P<0.05) to Cide proteins expression in liver (Cidea, R=.536; Cidec, R=.590), adipose tissue (Cidea, R=.618), and skeletal muscle (Cidea, R=.699; Cidec, R=.546). Area under the insulin assisted glucose tolerance curve (IAGT‐AUC), an indicator of insulin resistance, was also significantly related (P<0.05) to Cide expression in liver (Cidea, R=.810; Cidec, R=.763), adipose tissue (Cidea, R=.495; Cidec, R=.535), and skeletal muscle (Cidec, R=.827). Our findings indicate that changes in Cide expression are associated with diet‐induced obesity and insulin resistance and that exercise training may ameliorate diet‐induced obesity and preserve insulin action, in part, by preventing an increase Cide expression