Abstract The work presents modeling of interface phenomena in biological structures. Selected ways of numerical modeling of phenomena at the boundary of two materials by means of FEM methods are discussed. The work focuses on phenomena related to biological structures and their mutual interactions. Using an example of an implant-bone system, various techniques of modeling interface phenomena are compared and referred to experimental results. The study reveals the main features of the selected modeling techniques, e.g. complexity of creating the model, time-consumption of computation, reliability of the obtained results. The obtained results proved that the most advantageous method is the one that makes it possible to regard interactions as numerical values, without an excessive generation of the finite elements (the grid) at the materials boundary. The contact modeling technique based on the contact indicator showed the lowest value of standard deviation in relation to contact modeling techniques: with the use of elastic-damping elements, based on the so-called boundary slip line and based on the so-called bio-layer. The contact indicator should be understood as a numerical value describing the interaction of the boundary surfaces of two objects cooperating with each other. The value of the indicator was determined experimentally. The value have oscillated +/- 0.0012mm. This is a very small value knowing that the standard deviation for the modeling technique of the contact employing damping-elastic elements gives a spread of +/- 0,1442 mm.