The present article was conducted to evaluate the effect of in ovo injection of arginine on hatchability, immune system and caecum microflora of broiler chickens. For this reason, 300 fertile eggs were used in a completely randomized design with three experimental treatments. The experimental groups included: 1%–0.5% l‐arginine (100 eggs), 2%–1% l‐arginine (100 eggs), 3‐ control [included both sham control (injection of distilled water; 50 eggs) and control (no injection; 50 eggs)], which were injected on d 14 of incubation. After hatching, chicks of each experimental group (0.5% l‐arginine, 1% l‐arginine, and control groups) were randomly divided into four equal groups (as replicates) and reared for 30 days. Weight and feeding of chickens were recorded. Next, blood samples of chickens were collected on day 30 to evaluate antibody titre. Also, chickens were slaughtered on 24 and 30 days of the experiment to evaluate immune system organs and caecum microflora. Based on the results, in ovo injection of l‐arginine had no significant effect on hatchability, body weight, antibody titre, spleen, bursa of Fabricius and thymus weight (p > .05). On the other hand, treatments significantly affected feed intake and feed conversion ratio (p < .05). As a novel finding, in ovo injection of l‐arginine increased caecal Lactobacillus (p < .01), while decreasing Coliform and Escherichia Coli bacteria (p < .01). However, treatments did not influence caecal Enterococcus (p > .05). The overall results indicated that in ovo injection of 0.5% l‐arginine had a better improving effect on caecal microflora and then considered as a recommended level of the present experiment.