Mitochondria and chloroplasts contain their own genetic complement. Eukaryotic cells must establish mechanisms by which the organellar and nuclear genomes are co-ordinately expressed. In the yeast S. cerevisiae, mitochondrial mutants that have respiratory deficiencies have altered patterns of nuclear gene expression. In strains that are deficient in the mitochondrial isoform of citrate synthase there is an up-regulation of the peroxisomal isoform. There is evidence that the mitochondria send a signal to the nucleus which results in the increased expression of the peroxisomal form of citrate synthase. Oxygen induces the biosynthesis of haem. When yeast are grown in aerobic culture, mitochondrial haem is transduced to the nucleus where it induces the expression of nuclear genes which encode proteins important for cellular respiration. Plant cells in which the chloroplasts have suffered photo-oxidative damage do not express nuclear genes that encode photosynthetic protein. Genetic studies in Arabidopsis have resulted in the characterization of mutants that do express nuclear photosynthetic genes when the development of the chloroplast is inhibited. These mutants will be instrumental in identifying the components of the chloroplast-to-nucleus signal-transduction pathways in plant cells. The identity of the signal that informs the nucleus of the developmental site of the chloroplast is unknown. Chlorophyll precursors, haem and porphyrin are considered candidate signal molecules. Recent studies have implicated that the redox state of the plastoquinone pool in chloroplasts may be involved in regulating nuclear gene expression. These studies have also shown that kinases and phosphatases may participate in relaying signals to the nucleus about the functional state of the chloroplast.