Within this contribution, we demonstrate a combination of microarrays, microfluidics and SERS to enable a sequence specific detection of DNA. In this combination, the microarray allows for the immobilisation of DNA sequences as well as the removal of unbound DNA, microfluidics permit the automation of the process and SERS provides a highly sensitive detection by means of an interaction between an analyte molecule and the enhanced electromagnetic field in the proximity of metallic nanostructured surfaces such as spherical nanoparticles. With this setup, we are able to distinguish between different complementary and non-complementary target sequences in one sample solution.