A method for isolating microbial cells from a blood sample containing or suspected of containing one or more microorganisms, the method comprising: providing an aqueous solution comprising a blood sample from a higher eukaryotic organism; adding a first selective lysis reagent to the aqueous solution for a time period sufficient to lyse most of the erythrocytes and release hemoglobin therefrom, wherein the integrity of at least most microbial cells and leukocytes in the blood sample are preserved; separating and removing from the aqueous solution at least a portion of the higher eukaryotic proteins, including hemoglobin, while preserving most or all of the microbial cells; adding a second selective lysis reagent to the aqueous solution; incubating the aqueous solution for a time period sufficient to lyse leukocytes in the blood sample and release therefrom higher eukaryotic DNA, wherein the integrity of at least most microbial cells in the blood sample is preserved; providing an endonuclease to the aqueous solution, and incubating the aqueous solution for a time period sufficient to lyse higher eukaryotic DNA; adding to the aqueous solution a magnetic bead, and at least one of a water soluble polymer and at least one inorganic salt in a quantity sufficient to cause blood plasma, blood cell components and microorganisms to displace directly or indirectly onto the magnetic bead; separating microbial cells displaced onto the magnetic bead from the aqueous solution; washing the separated microbial cells one or more times with a wash solution, wherein the wash solution comprises at least one of a water soluble polymer and an inorganic salt; eluting microbial cells from the magnetic bead by incubating the sample with a solution comprising at least one protease; and isolating released microbial cells from the magnetic bead and from at least a portion of the residual blood components in the solution. providing an aqueous solution comprising a blood sample from a higher eukaryotic organism; adding a first selective lysis reagent to the aqueous solution for a time period sufficient to lyse most of the erythrocytes and release hemoglobin therefrom, wherein the integrity of at least most microbial cells and leukocytes in the blood sample are preserved; separating and removing from the aqueous solution at least a portion of the higher eukaryotic proteins, including hemoglobin, while preserving most or all of the microbial cells; adding a second selective lysis reagent to the aqueous solution; incubating the aqueous solution for a time period sufficient to lyse leukocytes in the blood sample and release therefrom higher eukaryotic DNA, wherein the integrity of at least most microbial cells in the blood sample is preserved; providing an endonuclease to the aqueous solution, and incubating the aqueous solution for a time period sufficient to lyse higher eukaryotic DNA; adding to the aqueous solution a magnetic bead, and at least one of a water soluble polymer and at least one inorganic salt in a quantity sufficient to cause blood plasma, blood cell components and microorganisms to displace directly or indirectly onto the magnetic bead; separating microbial cells displaced onto the magnetic bead from the aqueous solution; washing the separated microbial cells one or more times with a wash solution, wherein the wash solution comprises at least one of a water soluble polymer and an inorganic salt; eluting microbial cells from the magnetic bead by incubating the sample with a solution comprising at least one protease; and isolating released microbial cells from the magnetic bead and from at least a portion of the residual blood components in the solution.