In the first part of this review, the biochemistry of lipid accumulation in the oleaginous microorganisms is depicted. Lipid biosynthesis form sugars and related substrates is a secondary anabolic activity, conducted after essential nutrient (usually nitrogen) depletion in the medium. Due to this exhaustion, the carbon flow is directed towards the accumulation of intracellular citric acid that is used as acetyl-CoA donor in the cytoplasm. Acetyl-CoA generates cellular fatty acids and subsequently triacylglycerols. Lipid accumulation from hydrophobic substrates is a growth associated process, being independent from nitrogen exhaustion in the medium. Medium fatty acids are incorporated with various incorporation rates and are either dissimilated for growth needs or become “substrate” for intracellular biotransformations. “New” fatty acid profiles (in both extra- and intracellular lipids) that did not previously exist in the medium are likely to be produced. Oleaginous microorganisms consume their own storage lipids when their metabolic abilities cannot be saturated by the extracellular carbon source. Reserve lipid breakdown is independent from the type of the carbon source used for lipid accumulation. In most cases it is accompanied by lipid-free biomass production. Lipid mobilization is a specific process, as preferential degradation of the neutral lipid fractions is observed.