We investigated the potential links between stomatal control of transpiration and the risk of embolism in root and shoot xylem of seedlings of three Mediterranean conifers (Cupressus sempervirens, Pinus halepensis and P. nigra) grown in a greenhouse under semi-controlled conditions. We measured the intrinsic vulnerability to embolism in roots and current year shoots by the air injection method. Root and shoot segments were subjected to increasing pressures, and the induced loss of hydraulic conductivity recorded. The three species displayed very different vulnerabilities in shoots, with P. nigra being much more vulnerable than P. halepensis and C. sempervirens. Roots were distinctly more vulnerable than shoots in C. sempervirens and P. halepensis (50% loss of conductivity induced at 3.0 MPa and 1.7 MPa higher xylem water potential in roots vs shoots). In P. nigra, no significant difference of vulnerability between shoots and roots was found. Seedlings were subjected to soil drought, and stomatal conductance, twig hydraulic conductivity and needle water potential were measured. The water potential resulting in almost complete stomatal closure (90%) was very close to the threshold water potential inducing loss of conductivity (10%) in twigs in P nigra, resulting in a very narrow safety margin between stomatal closure and embolism induction. The safety margin was larger in P. halepensis and greatest in C. sempervirens. Unexpectedly, this water potential threshold produced a 30–50% loss of conductivity in 3–5 mm diameter roots, depending on the species. The implications of this finding are discussed.