A highly parallel microarray scanner for functional genomic research using a dynamically reconfigurable holographic excitation and hyperspectral fluorescence detection is described. The light from two laser sources (405 and 532 nm) is split into an arbitrary number of focused spots on the biochip using a pair of spatial light modulators and a novel imaging system. The parallel optical scanner includes a hyperspectral detection unit with a high-sensitivity CCD camera to detect and analyze the emitted fluorescence spectra (from 430 to 800 nm) of all illuminated spots simultaneously. By using an xy scanner, the spectra of all spots on an entire array can be read out line by line.