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The Micromegas (μM) detector is one of the three types of detectors (CCD, μM and TPC) that are used for solar axion detection at the CAST experiment. The μM detector is sensitive to X-rays, originating from a conversion of axion to photon in a strong magnetic field (9T), in the range of a few hundred eV to 10 keV. Good detection efficiency, energy resolution, spatial resolution and extremely low background are the characteristics of this type of detector. The Data Acquisition of the Micromegas detector is presented here. The Front End cards are using multiplexed analog integrated circuits. A set of VME modules performs the readout that is expandable to read up to 2 × 19 × 2048 (77824) channels. The system has the capability to apply online, per individual channel, a threshold and a subsequent pedestal subtraction. At the CAST experiment rates the dead time is negligible. A PCI-MXI2-VME interface is used to read out the data to a PC, to perform monitoring and to Display Events. The system is based on the National Instruments' LabView software and is running both in Windows 2000 and Linux operating systems. The data are automatically archived on storage media at the central CERN computing facilities and the PC clock is synchronized periodically with the GPS time using the CERN time servers. This allows the precise event time stamping for the possibility to correlate them to astrophysical phenomena. The precision of the clock update is of the order of 50 μs. The same system has been used for Medical Imaging R&D programs and Dark Matter searches.