The role of sugars as regulatory signals has mainly focused on their effects on plant growth, development, gene expression, and metabolism. Little, however, is known about their role in controlling secondary metabolism. Previous work in our lab showed that sugars affect the production of the sesquiterpene antimalarial drug, artemisinin, in hairy roots of Artemisia annua. In this study, sugars alone or in combination with their analogues were used to investigate if sugars control artemisinin production in Artemisia annua seedlings. Compared to sucrose, a 200% increase in artemisinin by glucose was observed. When the glucose analog, 3-O-methylglucose, which is not phosphorylated effectively by hexokinase, was added with glucose, artemisinin production was dramatically decreased but hexokinase activity was significantly increased compared to glucose. In contrast, neither mannose, which can be phosphorylated by hexokinase, nor mannitol, which can not be transported into cells had any significant effect on artemisinin yield. When different ratios of fructose to glucose were added to seedlings, artemisinin yield was directly proportional to glucose concentration. Although addition of sucrose with glucose gave inconclusive results, sucrose analogues decreased artemisinin production compared to sucrose. These results suggested that both monosaccharide and disaccharide sugars may be acting as signal molecules thereby affecting the downstream production of artemisinin. Taken together, these experiments showed that sugars clearly affect terpenoid production, but that the mechanism of their effects appears to be complex.