Spermatogenesis is a tightly regulated, selenium-dependent process. Nutritional deficiencies, including Se, have been associated with decreased fertility. During Se depletion, testes preferentially retain Se while other tissues are depleted. This study was aimed at evaluating the effect of Se source (inorganic or organic yeast derived) on testes weight, Se content, and gene expression. At 17 weeks of age, roosters were randomly assigned to one of three treatments: basal diet (control), basal diet + 0.3 mg organic Se/kg organic yeast-derived Se (YS; Sel-Plex®, Alltech Inc.), or basal diet + 0.3 mg inorganic Se /kg inorganic Se as sodium selenite (SS). At 40 weeks of age, seven roosters from each treatment were euthanized and testes removed. Testes weight did not differ between treatments, but Se content was greater (P ≤ 0.01) in YS than SS and control. Testicular differential gene expression profiling was accomplished using the Affymetrix Genechip® chicken genome array. Ingenuity® pathway analysis revealed that Se supplementation, regardless of source, results in the up-regulation of genes governing cell structure/morphology. The enrichment of such pathways was greater with YS than SS. These expression patterns suggest that aside from playing a role in antioxidant defense, Se, especially in the organic YS form, is useful for maintaining testicular cell structure.