For a long time, occurrence and nature of sulfite oxidase activity in higher plants were controversially discussed. During primary sulfate assimilation in the chloroplast, sulfate is reduced via sulfite to organic sulfide, which is essential for cysteine biosynthesis. However, it has also been reported that sulfite can be oxidized back to sulfate, e.g. when plants were subjected to SO2 gas. Recently, work from our laboratory has identified the sulfite oxidase as the fourth member of molybdenum-enzymes in plants. Here we discuss how nature separates the two counteracting pathways--sulfate assimilation and sulfite detoxification--into two different cell organelles and we will also discuss how these two processes are coregulated.