Homeostasis of nitrogen, phosphorus and sulfur in growing plants requires a sustained intake of these elements into root cells. Under most situations, the adjustment of root N, P or S acquisition to the nutrient demand of the plant is hampered by the limiting and fluctuating availability of these elements in the soil. To cope with this constraint, higher plants modulate their root uptake capacity to compensate for the changes in external concentrations of the N, P or S sources. This adaptive response relies on both physiological and morphological changes in the root system, triggered by nutrient-specific sensing and signalling pathways. The underlying molecular mechanisms now begin to be elucidated. Key root membrane transport proteins have been identified, as well as molecular regulators that control root uptake systems or root system architecture in response to N, P or S availability. Significant but yet poorly understood interactions with carbon or hormone signalling have been unravelled, opening new routes for integrating the mechanisms of nutrient homeostasis into the whole plant.