Analysis of bacterial DNA from fecal samples of mice is commonly performed in experimental studies. Although DNA extraction is a critical step in various molecular approaches, the efficiency of methods that may be used for DNA extraction from mice fecal samples has never been evaluated. We compared the efficiencies of six widely used commercial kits (MasterPure (TM) Gram Positive DNA Purification Kit, QIAamp (R) DNA Stool Mini Kit; NucliSENS (R) easyMAG (R), ZR Fecal DNA MiniPrep (TM), FastDNA (R) SPIN Kit for Feces and FastDNA (R) SPIN Kit for Soil) and a non-commercial method for DNA isolation from mice feces and cecal contents. DNA quantity and quality were assessed by fluorometry, spectrophotometry, gel electrophoresis and qPCR. Cell lysis efficiencies were evaluated by qPCR targeting three relevant bacteria in spiked specimens. For both feces and intestinal contents, the most efficient extraction method was the FastDNA (R) SPIN Kit for Soil.