By using a focused laser beam as the light source of the microscope, to minimized flare, together with a pinhole in front of a photo detector to eliminate out-of-focus data, the confocal laser scanning microscope (CLSM) provides a depth-discriminated fluorescence image with high spatial resolution. The CLSM, therefore, has been widely used as a tool for accurate morphometric and densitometric analyses. We discussed here the biological applications of CLSM for demonstrating the three-dimensional features of the embryonic heart tube and chromosome and for imaging fast dynamic changes of [Ca2+]i in the living heart muscle cell pairs.