We investigated the transcriptome of four albina (alb-e16 and alb-f17) and xantha (xan-s46 and xanb12) barley mutants to provide an overall transcriptional picture of genes whose expression is interconnected with chloroplast activities and to search for candidate genes associated to the mutations. About 20% of the genes expressed in leaf cells showed a modified expression level in the mutants. Beside those encoding plastid localized proteins, more than 3000 genes involved in non-chloroplast localized metabolism were up-/downregulated in the mutants revealing the network of chloroplast dependent metabolic pathways. Some keys metabolic pathways (e.g. chlorophyll or carotenoids biosynthesis) have been studied verifying the induction or repression of subsequent steps and the intermediates and pigment content. This permitted us to identify steps of pigment biosynthesis not functional in mutants and different subregulons of genes regulated as pigment synthesis proceeded.