The study was done on 120 newly hatched brown Japanese quail obtained from local Egyptian hatcheries, randomly divided into two groups. The 1st group was reared on cage system (CS), and 2nd group was reared on floor system (FS) (60 chicks per group/ 3 replicates, 20 chick/replicate), to investigate the effect of housing on the hygiene, performance, survivability, and economic efficiency of quails. The results showed that the total aerobic bacteria (TAB) of cloacal swabs had non-significant differences between CS, and FS. The higher TAB, E. coli, and total fungal count (TFC) were recorded in FS in feed, water, litter, and floor swabs samples, CS was more hygienic rearing system for quails. Moreover, the higher TAB, E. coli, and lactobacillus were recorded in intestinal samples collected from quails on FS (Log10 CFU/g 5.34, 4.47, and 3.96, respectively). There were no significant difference in immunoglobulin G, interleukin 2 & 6, Malondialdehyde, Superoxide Dismutase, and catalase activity between both rearing systems. Regarding performance parameters, the higher body weight, and feed consumption were achieved in Japanese quails reared on FS. Moreover, the rearing system had no significant influence on the performance, and carcass traits. From the economic point of view, FS had higher feed cost, total variable cost, total cost, and cost of each kg body weight gain from feed than those reared on CS. While, the net profit, gross margin, benefit cost ratio, return on investment, and net profit for each kg body weight gain were non-significantly higher in CS than FS.