Disclosed herein are systems and methods for detecting potentially malicious changes in an application. In one aspect, an exemplary method comprises, selecting a first file to be analyzed and at least one second file similar to the first file, for each of the at least one second file, calculating at least one set of features, identifying a set of distinguishing features of the first file by finding, for each of the at least one second file, a difference between a set of features of the first file and the calculated at least one set of features of the second file, and detecting a presence of potentially malicious changes in the identified set of distinguishing features of the first file.