The ability of Java Cards to withstand attacks is based on software and hardware countermeasures, and on the ability of the Java platform to check the correct behavior of Java code (by using byte code verification). Recently, the idea of combining logical attacks with a physical attack in order to bypass byte code verification has emerged. For instance, correct and legitimate Java Card applications can be dynamically modified on-card using a laser beam. Such applications become mutant applications, with a different control flow from the original expected behaviour. This internal change could lead to bypass controls and protections and thus offer illegal access to secret data and operations inside the chip. This paper presents an evaluation of the application ability to become mutant and a new countermeasure based on the runtime checks of the application control flow to detect the deviant mutations.