Malaria mortality continues to increase across the world and represents the most important parasitic disease of man. Artemisia annua L. (Asteraceae) has been used to treat fevers in China for over two millennia and recently the clinical efficacy of teas and decoctions derived from this species have been demonstrated, using high artemisinin-yielding plants. Therefore, it is important to verify the artemisinin levels in local cultivations in areas where malaria is endemic and to assess how different geographical and climatic conditions may affect the efficacy of traditional treatments. In this study, samples of the aerial parts of A. annua (ANAMED 3 hybrid) cultivated in three different locations in Burundi were compared for their content of active principles. Artemisinin levels in the plant materials ranged from 0.20% to 0.35%, while total flavonoid contents ranged from 0.32% to 0.80%.