The aim of this study is to compare between the count of Bifidobacterium spp. and Lactobacillus spp. as probiotic in stool of both autistic and non-autistic children. Bifidobacterium spp. and Lactobacillus spp. were assessed in stool samples of 40 autistic children and 20 healthy typical children of similar ages which consider as control group. The study indicated that the counts of both Bifidobacterium spp. and Lactobacillus spp. were lower in the stool of autistic children than that of their control group. It was significant in the case of Lactobacillus spp. with (p value 0.05) and highly significant in the case of Bifidobacterium spp. with (p value 0.000) and the count of bacteria wasn't affected by sex (male or female).