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The formation of nonluminescent aggregates of aluminium sulfonated phthalocyanine in complexes with CdSe/ZnS quantum dots causes a decrease of the intracomplex energy transfer efficiency with increasing phthalocyanine concentration. This was confirmed by steady-state absorption and photoluminescent spectroscopy. A corresponding physical model was developed that describes well the experimental data. The results can be used at designing of QD/molecule systems with the desired spatial arrangement for photodynamic therapy.