The effects of waterborne uranium (U) exposure on gene expression were examined in four organs (brain, liver, skeletal muscles, and gills) of the zebrafish (Danio rerio). Adult male fish were exposed to three treatments: No added uranium (control), 23 ± 6 μg U/L, and 130 ± 34 μg U/L. After 3, 10, 21, and 28 d of exposure and an 8-d depuration period, gene expression and uranium bioaccumulation were analyzed. Bioaccumulation decreased significantly in liver during the depuration phase, and genes involved in detoxification, apoptotic mechanism, and immune response were strongly induced. Among these genes, abcb3l1, which belongs to the adenosine triphosphate (ATP)—binding cassette transporter family, was induced 4- and 24-fold in organisms previously exposed to 23 ± 6 and 130 ± 34 μg U/L, respectively. These results highlight the role of liver in detoxification mechanisms. In gills, at the highest uranium concentration, gpx1a, cat, sod1, and sod2 genes were up-regulated at day 21, indicating the onset of an oxidative stress. Mitochondrial metabolism and DNA integrity also were affected, because coxI, atp5f1, and rad51 genes were up-regulated at day 21 and during the depuration phase. In skeletal muscles, coxI, atp5f1, and cat were induced at day 3, suggesting an impact on the mitochondrial metabolism and production of reactive oxygen species. In brain, glsI also was induced at day 3, suggesting a need in the glutamate synthesis involved with neuron transmission. No changes in gene expression were observed in brain and skeletal muscles at days 21 and 28, although bioaccumulation increased. During the depuration phase, uranium excretion was inefficient in brain and skeletal muscles, and expression of most of the tissue-specific genes was repressed or unchanged.