This experiment evaluated the effects of Saccharomyces cerevisiae (S. cerevisiae) and citric acid on production performance, egg quality, intestine histomorphology, and avian β-defensin 1 and 2 (AvBD 1 and 2) gene expressions in laying Japanese quails. A total of 400 48-day-old quails were randomly assigned to a 2×2×2 factorial arrangement of treatments with 5 replicates (each containing 10 quails) for 7 weeks. Variable factors consisted of S. cerevisiae (0 and 100 mg/kg diet), citric acid (0 and 5 g/kg diet), and Virginiamycin (0 and 50 mg/kg diet). At the completion of the trial, one bird per replicate was randomly killed, and jejunal tissue samples were removed to evaluate intestinal morphometric characteristics. Samples were taken from the midpoint of the jejunum to measure the gene expression of AvBD 1 and 2. Dietary inclusion of both S. cerevisiae and citric acid resulted in increased egg weight, egg mass, reduced feed intake, and improved FCR (p<0.05). The addition of S. cerevisiae to diets containing citric acid reduced feed intake, increased egg weight, and improved FCR (p<0.05). Shell weight and shell thickness were increased in birds fed each of S. cerevisiae and citric acid supplements (p<0.05). Dietary S. cerevisiae and citric acid similarly increased intestinal villus height, width, surface area, and the villus height to crypt depth ratio (p<0.0001). Results showed that AvBD 1 and 2 genes expression were up-regulated on quails fed S. cerevisiaesupplemented diets (p<0.0001). In conclusion, these results suggest that supplementation of S. cerevisiae and citric acid as functional feed additives either alone or in combination could be a potential alternative to antibiotics in the diet of Japanese laying quails.