The employee evaluation is one of the key activities of human resources management in organizations. The result of this process influences career, motivation and rewarding. Management by objectives, behaviorally anchored rating scales, comparative methods or assessment centre are methods used in employee evaluation in organizations. Some supplementary methods can be applied. The aim of this paper is to introduce employee evaluation, the analytic hierarchy process and the eigenvector method briefly and to apply this method in a case study. The case study demonstrates employee evaluation process in one medium-sized enterprise focused on high-tech. The usual way of determining results applied in the selected company is total sum of points. Modification of this procedure by eigenvector method is suggested in this paper. This modification takes different priorities of factors in consideration. Results gained by both methods are compared.