In the current study, the effect of kefir upon the performance, intestinal microflora and histopathology of certain organs in laying hens was investigated. Totally, 108 Lohmann Brown layers, aged 24 weeks, were allocated randomly into three groups, as; Group C (control, n=36): no treatment, Group A (n=36): 10 cc, and Group B (n=36): 7.5 cc kefir per litre of water. Animals were fed for 10 weeks with basal diets. Livers showed moderate level of hydropic degeneration, some lipidosis and focal haemorrhages with high amounts of kefir (Group A). Fewer active follicles in the ovarium were also observed in this group. The egg yield was significantly (P<0.01) lower in Group A (89.40±0.91) than in Group C (92.50±0.83) and Group B (92.86±0.87). For the pH of large intestines, unlike the small ones, it was significantly changed (P<0.01) from basic to acidic milieu in kefir-treated groups. The titres of coliform (E. coli), aerobic (Lactobacillus spp.), and anaerobic bacteria (Peptostreptococcus spp.) were significantly decreased (P<0.05 to P<0.001) with increased intake for both intestinal tracts. We conclude that; i) high kefir intake could unfavourably impair the digestive organ structures, ii) the supplementations led to a marked decrease in the large intestinal pH and microbiological load of the intestines, and iii) high kefir level markedly decreased the egg yield, unlike the low concentration as leading to a considerable improvement from the 6th weeks onwards.