Imperative for a sensible use of DNA-chips is the establishment of standardised procedures and processes for a comparable and compatible data production, quality control and analysis. To this end, we have established a surface chemistry for the covalent attachment by both immobilisation and in situ synthesis of DNA molecules on glass or polypropylene. Apart from stable bonding of more than 30 consecutive hybridisations, parameters like loading capacity, charge and hydrophobicity can be modified in a controlled manner. For photolithographic oligomer synthesis, we developed a chemistry that yields quantitative efficacy of each condensation reaction. In addition, a procedure was set up allowing for an accurate measurement of yield and amount at all individual positions of every oligomer chip prior to subsequent uses of the very chip. Substitution of PNA for DNA molecules on the arrays combined the high selectivity of oligomers with the strong duplex stability of PCR-products at hybridisation conditions which prevent double-strand formation between the DNA probes. Lastly, we are working on technology to replace optical detection by a system not requiring labelling nor PCR-amplification of probe material even from limited samples prior to quantitative on-line detection.