The analysis of the spatial expression patterns of genes is important for deciphering their functions. In situ hybridization provides insight into gene expression patterns at the cellular level. Here we describe a procedure for performing in situ hybridization on sections of paraffin-embedded tissue, including synthesis of labeled RNA probes, hybridization of the probes with target mRNAs, and immunological detection of the signals. The method enables evaluation of the expression patterns of genes in a variety of tissues of rice.