With 3 figures and 1 table Abstract Evaluation of transgenic plants during their development is of major importance for breeders. To facilitate this evaluation, we applied a real‐time, reverse transcription polymerase chain reaction method to maize tissues that allows quantitative expression profiling of transgenes. To obtain consistent results, sampling, transport, storage and extraction protocols were standardized for a wide range of samples (leaves, stems, roots, pollen and kernels) and phenological stages (from the 4–6 leaves stage to physiological maturity). RNA integrity was monitored by Agilent 2100 Bioanalyzer to ensure that decomposed RNA samples were excluded from further study. A simple and effective SYBR Green methodology was applied for relative quantification of transgene expression. Several endogenous controls were tested to achieve the best possible results. Quantitave results presented illustrate the application of our protocol to the quantification of cry3Bb1 (encoding corn root worm resistance) expression in MON88017 event derived transgenic maize lines. The methodology described here can be routinely performed for the quantification of gene expression in maize.