In order to study spatial arrangement and dynamics of chromosomes and nuclear structures, we have developed a computerized fluorescence microscope workstation. This microscope workstation is capable of rapidly acquiring three-dimensional, multiple-wavelength image data and allows accurate reconstructions of three-dimensional cellular structures stained with multiple fluorescent dyes. Using this microscope system, we have examined dynamics of chromosomes and microtubules in mammalian culture cells by combination of high-resolution analysis in fixed specimens and time-lapse analysis in living cells. A key aspect of such microscopic approaches is a capability of detecting transient events during dynamic biological processes.