Microcapsules consisting solely of biocompatible components were prepared in water by a colloidal templating technique on soluble carbonate cores using alginic acid sodium salt, protamine sulfate, dextrane sulfate, and chitosan. These microcapsules, as well as capsules made from synthetic polyelectrolytes, were labeled with water-soluble CdTe nanocrystals (NCs) emitting in the visible and, for the first time, with CdxHg1-xTe or HgTe NCs emitting in the near-IR. The luminescence efficiency of NCs at physiological conditions remained stable for two weeks in the case of CdTe and at least for a month for CdHgTe and dropped by 80% for HgTe because of the shift of the luminescence band outside the water transmission window. Biocompatible microcapsules labeled with CdxHg1-xTe NCs emitting at 750−1200 nm might be of special interest for monitoring the drug delivery processes.