The widespread application of confocal laser scanning microscopy has revolutionized biological imaging. We have developed a protocol for using confocal microscopy to examine the development of wild type and mutant Arabidopsis thaliana, overcoming the technical difficulties associated with examining whole-mounted plant tissue. This allowed us to rapidly determine the underlying cellular defects that lead to the morphological changes visible in several mutants, and has led to a greater understanding of the mechanisms involved in the control of floral organ number.