Acceleration of the drug discovery process in pre-clinical pharmaceutical research is a highly desirable goal and combinatorial chemistry united with automation technology promised to accomplish this task. Through the accumulation of experience with automated devices over time it became evident that only by harmonisation and streamlining of work-flow procedures the efficiency of the overall process can be improved. An open architecture of efficient data management and appropriate utilisation of automated laboratory protocols provides the opportunity to react in a flexible and advisable way. Only an integrative workflow concept promotes the enhancement of the overall performance. However, the foundation of any efforts towards the accelerated synthesis of new and desired compound arrays lies in the development of reliable chemistry protocols amenable to solid- and solution phase chemistry.