Biological medicines have introduced a new set of quality and safety issues because these medicinal products are large molecules synthesized in complex biological processes and may have pharmacodynamic properties that need extra consideration and study for safe administration to humans. A complex manufacturing process and molecular structure means that the exact identity of the material cannot be guaranteed by analytical technology alone but requires a well understood and reproducible manufacturing process. Furthermore, the production systems utilizing recombinant DNA technology in living cell systems are influenced by a multitude of factors that are not easily controlled. The result is that identity between manufactured lots of one product or between similar products (i.e., biosimilars) is difficult to confirm. Purification and analytical methods such as HPLC, CE, UPLC, SEC, ELISA, ELISpot, SPR and the transgenic mouse immunogenicity model are briefly reviewed as means of achieving the highest possible degree of safety for patients using biological medicines.