A system for the automated extraction of nucleic acids from nucleic acids containing samples, comprising at least one set of three plates (18, 19, 21), each of which having plural cavities, including a process plate for processing said nucleic acids, a reagent plate for providing reagents for mixing with said samples and an output plate for outputting said extracted nucleic acids, wherein said samples are contained in cavities of said process plate, comprising: a reagent pipetting device comprising a plurality of reagent pipettes provided with re-usable pipette tips repeatedly used for providing said reagents in said cavities of said reagent plate, wherein the re-usable pipette tips are fixedly secured to the reagent pipettes and are made of a metallic material; a sample pipetting device comprising a plurality of sample pipettes provided with disposable pipette tips for pipetting of said reagents from said cavities of said reagent plate to said samples contained in said cavities of said process plate to obtain sample-reagent mixtures and for transferring extracted nucleic acids containing fluids from said cavities of said process plate to said cavities of said output plate, an incubating device (24, 25) for incubating said sample-reagent mixtures in said cavities of said process plate to release the nucleic acids; a separating device for separating said released nucleic acids in said cavities of said process plate to obtain said extracted nucleic acids containing fluids; a controller for controlling steps to extract nucleic acids from said nucleic acids containing samples, configured to control: repeatedly using the re-usable pipette tips of the reagent pipetting device for providing reagents in cavities of said reagent plate; transferring the reagents to the samples using the disposable pipette tips of the sample pipetting device to obtain sample-reagent mixtures; incubating the sample-reagent mixtures in cavities of the process plate using the incubating device (24, 25) to release the nucleic acids to obtain released nucleic acids containing fluids; separating the released nucleic acids contained in the released nucleic acids containing fluids in cavities of the process plate using the separating device to obtain extracted nucleic acids containing fluids; and transferring the extracted nucleic acids containing fluids to cavities of the output plate using the disposable pipette tips of the sample pipetting device; wherein the number of cavities containing said samples is equal to the number of cavities containing said reagents, wherein each of said samples is assigned one-to-one to a cavity of said reagent plate, at least one disposable pipette tip and a cavity of said output plate. a reagent pipetting device comprising a plurality of reagent pipettes provided with re-usable pipette tips repeatedly used for providing said reagents in said cavities of said reagent plate, wherein the re-usable pipette tips are fixedly secured to the reagent pipettes and are made of a metallic material; a sample pipetting device comprising a plurality of sample pipettes provided with disposable pipette tips for pipetting of said reagents from said cavities of said reagent plate to said samples contained in said cavities of said process plate to obtain sample-reagent mixtures and for transferring extracted nucleic acids containing fluids from said cavities of said process plate to said cavities of said output plate, an incubating device (24, 25) for incubating said sample-reagent mixtures in said cavities of said process plate to release the nucleic acids; a separating device for separating said released nucleic acids in said cavities of said process plate to obtain said extracted nucleic acids containing fluids; a controller for controlling steps to extract nucleic acids from said nucleic acids containing samples, configured to control: repeatedly using the re-usable pipette tips of the reagent pipetting device for providing reagents in cavities of said reagent plate; transferring the reagents to the samples using the disposable pipette tips of the sample pipetting device to obtain sample-reagent mixtures; incubating the sample-reagent mixtures in cavities of the process plate using the incubating device (24, 25) to release the nucleic acids to obtain released nucleic acids containing fluids; separating the released nucleic acids contained in the released nucleic acids containing fluids in cavities of the process plate using the separating device to obtain extracted nucleic acids containing fluids; and transferring the extracted nucleic acids containing fluids to cavities of the output plate using the disposable pipette tips of the sample pipetting device;