1. The aim of study was to investigate whether the impact of the yeast Saccharomyces cerevisiae on the histological structure of the intestine, innervation of the small intestine wall, and basal biochemical serum parameters in Japanese quail was sex dependent. 2. One-day-old healthy male and female Japanese quail were fed either a basal diet containing no yeast (control group) or the basal diet plus 1.5% (15 g/kg of diet) of yeast (S. cerevisiae inactivated by drying). Samples from the duodenum and jejunum were taken from each bird at the age of 42 days. Blood samples were collected at this age and the concentrations of glucose, total protein, creatinine, uric acid, lipid profile (total cholesterol, low density lipoproteins (LDL), high density lipoproteins (HDL) and triacylglycerols (TG)), alanine aminotransferase (ALAT), aspartate aminotransferase (AspAT), lactate dehydrogenase (LDH), amylase (AMY), calcium, phosphorus and iron were determined. 3. Female quail fed diets supplemented with yeast had significantly lower total cholesterol and amylase activity than the control females. The concentration of HDL was higher in the male quail than in the females, irrespective of the treatment. An opposite effect was observed in LDL. The diet treatments influenced the activity of AspAT, which was significantly less in the male quail fed diets with 1.5% yeast. 4. Supplementation with S. cerevisiae increased the myenteron, submucosa and mucosa thickness, villus length and thickness and size of absorptive surface, while the number of villi and enterocytes were decreased in the duodenum in males. Female quail showed an increased absorptive surface in the jejunum. The Meissner (submucosal) plexuses were influenced by the feeding and sex to a greater extent than the Auerbach plexus (in the muscularis propria). 5. The results demonstrated that S. cerevisiae (1.5%) in the diet caused significant positive effects in Japanese quail, exerting an effect on the morphology of the small intestine in a sex-dependent manner.