A novel method to combine a microscope and an optical multichannel analyzer (OMA) into a microspectrophotometer (MSP) system is presented. In this system, an optical fiber was mounted into the image plane of the microscope both to collect light from the microscope and transmit it to the OMA for spectral analysis, as well as to conduct light in the reverse direction into the microscope for alignment purposes. The system is easy to construct, is simple to use, and has a higher spectral resolution than conventional MSPs without increasing the acquisition time. Its sensitivity depends on the photodetector used in the OMA. For the two application examples presented, (1) absorbance spectrum measurements of cytoplasm and nuclear areas of Papanicolaou-stained cervical cells and (2) autofluorescence spectrum measurements of different locations of unstained and unfixed skin tissue sections, this system was found to possess adequate sensitivity.