This study was conducted to investigate the effects of different levels of black cumin seeds (Nigella sativa L.) on performance, intestinal Escherichia coli count and morphology of jejunal epithelial cells in laying hens. A total of 100 Leghorn laying hens (Hy-Line W-36) of 49 weeks old were randomly distributed among five cage replicates of five birds each. Experimental diets consisted of different levels (0%, 1%, 2% and 3% of diet) of dietary black cumin inclusion. The experimental period lasted for a total of 10 weeks, and egg quality indexes and laying hens' performance were measured as two 35-day trial periods. At the final day, two hens per replicate were slaughtered to investigate the influence of dietary treatments on intestinal E. coli colonization and morphology of jejunal cells. Although dietary black cumin in all supplementation levels decreased (p < 0.05) the enumeration of ileal E. coli, the morphological and histological alterations in small intestine such as enhancement of villus height to crypt depth ratio, increased goblet cell numbers and proliferation of lamina propria lymphatic follicles were observed after dietary supplementation with at least 2% black cumin. Dietary treatments decreased (p < 0.05) the concentration of serum cholesterol and triglycerides and increased (p < 0.05) serum HDL concentration and relative weight of pancreas; however, the egg yolk cholesterol was not influenced by dietary treatments. In addition, dietary supplementation with black cumin improved (p < 0.05) eggshell quality and Haugh unit. The best feed conversion ratio was obtained when diets were supplemented with 2% black cumin. This improvement was due to the increase (p < 0.05) in egg mass and contemporaneous decrease (p < 0.01) in feed consumption. The present results indicated that regardless of supplementation level, dietary inclusion of black cumin decreased E. coli enumeration in ileal digesta and improved serum lipid profile and eggshell quality, whereas the best intestinal health indices and haying hens' performance were obtained by at least 2% black cumin seeds.