Fluorescence measurements on protein microarrays demand photodetectors with ultra-high sensitivity, low noise and parallel readout capability. A novel compact instrument capable of ultra-sensitive analysis of multiple proteins in a customized microarray has been designed and implemented. This system is based on a monolithic 6× 8 array of single photon avalanche diodes (SPADs). The SPAD detector technology combines the general advantages of silicon microelectronic devices (miniature size, ruggedness and reliability, low-voltage and low-power operation, insensitivity to magnetic fields, etc.) with very high sensitivity, due to the ability to detect single photons with high efficiency and low detector noise. For performing measurements of chemiluminescent microarrays, the necessary electronic and opto-mechanical set-up and the glass slide coating procedure for protein immobilization were developed. A viable methodology for specific detection of any protein is experimentally demonstrated.