A protocol is described for harvesting developing Arabidopsis thaliana seeds from the same stage and for RNA isolation in quality and quantity suitable for plastid gene expression analyses. The method is designed in order to decrease seed polysaccharides and polyphenolics content of the RNA samples. DNA is removed from RNA samples by DNase treatment. In our hands, about 50-80 µg of pure RNA (A260/A280: 1.90; A230/A280: 2.3) is obtained from 25-50 mg of fresh tissues. RNA prepared according to this protocol can be used for RT-PCR, primer extension or macro array experiments.