<p><strong>Background:</strong> The influence of soil nutrients on biosynthesis of secondary metabolites from tropical trees has been poorly investigated.</p><p><strong>Questions: </strong>Does<strong> </strong>the deprival of Ca<sup>2+</sup> and K<sup>+</sup> influence the production of pharmacologically active compounds in the seedling of <em>Calophyllum brasiliense</em>?</p><p><strong>Species study</strong>: <em>Calophyllum brasiliense</em> Cambess.</p><p><strong>Study site: </strong>Los Tuxtlas, Veracruz, Mexico; November 2005 to November 2009.</p><p><strong>Methods: </strong>The seedlings were obtained from seeds and subjected to different hydroponic treatments: 1) modified Hoagland solution (MHS), 2) MHS-Ca<sup>2+</sup>, and 3) MHS-K<sup>+</sup>. Growth, height, foliar biomass, and HPLC analysis were performed after 7 months.</p><p><strong>Results: </strong>Under hydroponic conditions Ca<sup>2+</sup> and K<sup>+</sup> deficiency induced the mortality of 53 % and 28 % of the seedlings, respectively. The foliar biomass, and plant height of the survivors were also drastically reduced. MHS-K<sup>+</sup> treatment induced a 15, 4.2 and 4.3-fold decrease for calanolides B, C, and apetalic acid in the leaves, respectively. MHS-Ca<sup>2+</sup> treatment induced a decrease of 4.3, and 2.4-fold for calanolide B, and C, respectively.</p><p><strong>Conclusion: </strong>Ca<sup>2+</sup> is essential for survival of <em>C. brasiliense</em> seedlings under hydroponic conditions, Ca<sup>2+</sup> and K<sup>+</sup> are critical for growth, foliar production, and biosynthesis of apetalic acid, and calanolide B.</p>