Abstract: A system and method for the automated extraction of nucleic acids from nucleic acids containing samples are disclosed. In the system, reagents provided in cavities of a reagent plate are transferred to samples accommodated in a process plate using a pipetting device comprising pipettes provided with disposable pipette tips for pipetting of the reagents to obtain sample-reagent mixtures, the sample-reagent mixtures accommodated in the process plate are incubated by an incubating device to release the nucleic acids; the released nucleic acids accommodated in the process plate are separated by a separating device and released to obtain extracted nucleic acids containing fluids; the extracted nucleic acids containing fluids are transferred to cavities of an output plate by disposable pipette tips; wherein each of the samples is assigned one-to-one to a cavity of the reagent plate, at least one of the disposable pipette tips and a cavity of the output plate.