Cytogenetic deficiencies in cotton lead to sporophytic semisterility due to the production of unbalanced gametophytes. Such deficiencies in cotton are not pollen transmissible because the chromatin deficient pollen lose viability. Several cytogenetic approaches have been used to detect cotton pollen viability and morphology. Electron microscopy is a valuable tool which provides in depth structural information but is a costly, tedious and labor intensive process. Recently, the development of the confocal laser scanning microscope (CLSM) has made it possible to overcome many of the problems associated with electron and conventional light microscopy to study pollen. The optical sectioning and digital image acquisition system in confocal microscopy makes it possible to reconstruct 3-dimensional images using a laser ray as a light source. (Continued)