Three different biological systems, the consortium of autotrophic bacteria Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans, heterotrophic fungus Aspergillus niger and heterotrophic yeast Rhodotorula mucilaginosa, were investigated for lithium extraction from lepidolite. The bacterial consortium was the most effective, 11 mg l-1 of Li was dissolved in the absence of nutrients within 336 days. Fungal and yeast bioleaching was faster (40 days), however, with lower extraction efficiency. Bioaccumulation represented a main process of Li extraction by R. mucilaginosa and A. niger, with 92 and 77% of total extracted Li accumulated in the biomass, respectively. The X-ray diffraction analysis for bioleaching residue indicated changes caused by microorganisms, however, with differences between bacterial leaching and bioleaching by fungi or yeasts. The final bioleaching yields for bacterial consortium, A. niger and R. mucilaginosa were 8.8%, 0.2% and 1.1%, respectively. Two-step bioleaching using heterotrophic organisms followed by autotrophic bioleaching could lead to the increase of the process kinetics and efficiency. Bioaccumulation of Li offers strong advantage in Li extraction from solution.