Peptide and protein PEGylation is usually undertaken to improve the biopharmaceutical properties of these drugs and, to date, several examples of conjugates with long permanence in the body as well as with localization ability in disease sites have been reported. Although a number of studies on the in vivo behavior and fate of conjugates have been performed, forecasting their pharmacokinetics is a difficult task since the pharmacokinetic profile is determined by a number of parameters which include physiological and anatomical aspects of the recipient and physico-chemical properties of the derivative. The most relevant perturbations of the protein molecule following PEG conjugation are: size enlargement, protein surface and glycosylation function masking, charge modification, and epitope shielding. In particular, size enlargement slows down kidney ultrafiltration and promotes the accumulation into permeable tissues by the passive enhanced permeation and retention mechanism. Charge and glycosylation function masking is revealed predominantly in reduced phagocytosis by the RES and liver cells. Protein shielding reduces proteolysis and immune system recognition, which are important routes of elimination. The specific effect of PEGylation on protein physico-chemical and biological properties is strictly determined by protein and polymer properties as well as by the adopted PEGylation strategy. Relevant parameters to be considered in protein-polymer conjugates are: protein structure, molecular weight and composition, polymer molecular weight and shape, number of linked polymer chains and conjugation chemistry. The examples reported in this review show that general considerations could be useful in developing a target product, although significant deviations from the expected results can not be excluded.