A synthesis process was reconsidered for encapsulating hydrophobic quantum dots (QDs) into silica capsules with high photoluminescent (PL) efficiency. The process comprises three steps: silanization of QD surfaces, seed formation by assembly of the QDs, and coating of the QD seeds with a silica shell. Analysis of the encapsulation mechanism enabled this process to be adapted for application to CdSe-based core-shell QDs with various organic ligands such as oleic acid and with various emission wavelengths. Formation of the seeds is the key step in synthesizing the silica capsules, so that they have high PL efficiency. Due to the differences in QD size and in the affinity of the ligands on their surfaces, the concentration of QDs used in the synthesis must be optimized to maximize emission efficiency. Contrary to an initial assumption, several ligands remained on the QD surfaces even after the QDs were transferred from organic solution to water. This greatly affected the size and PL efficiency of the seeds. Judicious selection of the conditions for seed and silica capsule synthesis resulted in seeds with PL efficiency greater than 70% and in silica capsules encapsulating multiple CdSe/CdZnS QDs with PL efficiency as high as 41%. Silica capsules incorporating QDs with various emission peak wavelengths from green to red were also prepared. The process presented serves as a guideline for encapsulating various types of hydrophobic QDs into silica capsules for biological tagging applications. (C) 2013 Elsevier Inc. All rights reserved.