In diseases such as cancer, Alzheimer’s disease or malaria, disease-related proteins take advantage of the heat shock protein (HSP) control system for their own activation or maturation. There is a quest to find inhibitors that specifically bind to the HSPs. Here, we report on a novel multiplexed assay system for inhibitor screening based on a protein microarray (MA) technique that was developed for routine applications with storable MAs. Purified HSPs are printed as full-length proteins on microarrays and used as a drug target for the screening of new inhibitors. Derivatives obtained by a combination of biological and chemical synthesis were tested as competitors of ATP with a suggested affinity for several HSP proteins which are hHSP from human, AtHSP83 (Arabidopsis thaliana) and HtpG from Helicobacter pylori. Some of these new derivatives exerted selectivity between human and bacterial heat shock proteins. Printed human HSP90 was used to test the binding of denatured proteins on the client binding site of human HSP90, since the full-length HSP maintains the capability to bind putative clients or cochaperones. Initial data revealed that the microarray application can be used to identify directly elevated heat-shock protein levels in cancer cell lysates. We suggest that microarray-based assaying of HSP levels can be used as a marker for determining stress levels.