The cause of Alzheimer's disease (AD) is still unknown. While research contributions identifying brain as locus of the disease is growing, evidence of severely impaired gastrointestinal (GI) functions with ageing too is accumulating, there is an equal dearth of information on GI tract in AD condition. The aim of this study was to assess the molecular, histological, morphological and microflora alterations of GI tract in male Alzheimer's transgenic mice. The present study also investigates the effect of dihydrotestosterone (DHT) treatment (1 mg/kg) on AD mice. Histoarchitecture data revealed a significant decrease in the villi number, muscular layer thickness, villi length, width, crypt length, enterocyte length and nuclei length. A shift in colon feces microbial community composition was observed by fatty acid methyl ester analysis. Amyloid precursor protein (APP) expression levels in intestine significantly increased in AD mice revealing its toxicity. DHT treatment attenuated the effect caused by AD on GI morphometrics, APP expression and colon micro flora population. These results for the first time reveal the quantitative and qualitative characteristics of GI tract in male Alzheimer's disease transgenic mice.