The study was carried out on eggs collected from 4 groups. Group I – Green leg (Gl) layers, kept in a free-range system, Group II –Lohmann Brown (LB) layers kept in a battery system, Group III –Lohmann Brown (LB) layers, kept in a free-range system, Group IV – Lohmann Brown (LB) layers, kept on litter containing straw and sawdust . Standard feeding system with the use of a DJ feed mixture containing 17% of protein and metabolic energy of 2800 kcal was applied. The layers were in the peak of laying, i.e. between 26 and 34 weeks of age. The purpose of the study was to find the effects of the breeding and housing systems on commercial quality of the eggs. The measurements included cystatin and lysozyme activities, as these substances are of great interest as regards their use in biomedical and nutraceutical applications. The measurements of the egg quality included: whole egg weight, the percentages of the egg-shell, white and yolk, the pH of albumen, Hough’s units and sensory analysis of the eggs. The essential goal was to determine lysozyme and cystatin activities, using standard methods. The highest activities were found in the eggs from the Lohmann layers, kept in cages, and in a floor system. The lowest values were obtained with the eggs of Green-leg layers, which could have been affected by the winter time. It is worth noting that the differences observed were significant. The effects of the genetic breed of the layers, feeding and housing systems and age of the hens on lysozyme and cystatin activities have been measured, but the results did not give us a unanimous answer to the problem under investigation. There is very great interest in obtaining lysozyme and cystatin from egg white and their application as nutraceutical or medical preparations. Industrial applications of the biologically active substances present in eggs are possible, provided that the problem of the differences in their activities in the raw material is solved. It is also important to know how to predict the values of these parameters.