Development of biochemical engineering has been presented. A typical bioprocess, which consists, besides the intrinsic process with the use of microorganisms, also of up- and down-stream processing has been described. The phenomena inside bioreactor in abiotic phase and inside microorganism cell have been analyzed. On the basis of metabolic stoichiometric models the principles of metabolic engineering, in particular metabolic flux analysis (MFA) and metabolic control analysis (MCA) have been given. The achievements of genetic engineering enabled proper implementation of metabolic modeling, exemplified by biosynthesis of recombinant protein. The importance of biochemical engineering for the future implementation of biotechnology has been emphasized.