Gene expression studies are often carried out at the whole organism, organ or tissue levels. The different cell types present in most tissue exhibit different patterns of gene expression. This limits analyses because results obtained represent an average of the activities of the different cell types, and may lead to masking of genes of interest that are specifically expressed in a particular cell type. The recent development of laser capture microdissection (LCM) now enables target cells to be isolated from complex tissues and allows analysis of specific cell types that represent the in vivo state at the time of sample extraction. LCM has been applied to analyse plant tissues in a number of studies. This review illustrates the application of LCM in studies on gene expression profiling and proteomics, and also in research on plant–microbe interactions.