Objective To investigate the dynamic changes of intestinal bacteria, endotoxin and liver function in autism rat models and patients. Methods (1) Sixteen SD rats of two weeks pregnant were randomly divided into group I (n=8), accepted intraperitoneal injection of valproic acid (VPA, 600 mg/kg), and group II (n=8), given same volume of saline by intraperitoneal injection; 3-4 weeks old new-born offsprings were respectively used as autism model group and control group (n=8); the autism models were confirmed by Morris water maze test;rats were executed, and liver function and endotoxin level in the peripheral blood were detected by automatic biochemical analyzer and kinetic turbidimetric assay, respectively; real-time fluorescence quantitative PCR was used in feces to detect long bifidobacterium, lactobacillus, clostridium perfringens and escherichia coli amount, and the value of intestinal resistance (B/E value) was compared and calculated. (2) Thirty children with autism and 30 normal controls, collected in our hospitals from January 2013 and January 2015, were chosen in our study; real-time fluorescence quantitative PCR was used in feces to detect long bifidobacterium, lactobacillus, clostridium perfringens and escherichia coli amount, and the value of intestinal resistance was compared and calculated. Results (1) As compared with control group, autism model group had significantly higher endotoxin level ([106.0±17.5] U/L vs. [42.0±10.4] U/L), glutamic-pyruvic transaminase and glutamic oxalacetic transaminase levels (P<0.05). Rats in the autism model group had significantly increased number of escherichia coli and clostridium perfringens, and significantly decreased number of lactobacillus and bifidobacterium as compared with control group (P<0.05); autism model group had significantly decreased intestinal fixed value (B/E<1) as compared with the control group (P<0. 05). (2) As compared with control subjects, children with autism had significantly increased number of escherichia coli and clostridium perfringens, and significantly decreased number of lactobacillus and bifidobacterium (P<0.05). Conclusion In valproate autism rat models, intestinal flora balance is broken, number of enterobacteriaceae and clostridium perfringens is increased, number of bifidobacterium and lactobacillus is decreased, and transaminase and endotoxin levels are increased; the same phenomenon of intestinal flora is also found in children with autism.