In the current research, the use of students' metacognitive strategies with and without special learning difficulties was studied as well as any differentiation of this use because of class or gender. The tool which was used was Junior Metacognitive Awareness Inventory, Version B (Jr. MAI) of Sperling et al. (2002) and is based on Brown's theoretical framework and includes the two dimensions of metacognition: "the knowledge of cognition" and "the regulation of cognition". It's the first time that the tool has been used in Greek student population of this age with and without special learning difficulties. Two hundred and forty students (245) participated in this research, 58 students with special learning difficulties and 187 students without special learning difficulties. The students of the two groups of the 5th and 6th grade presented several similarities regarding their preference in the use of the knowledge of cognition. The differentiation which appears in the rates is mainly quantitative and refers to the frequency of the use of strategies and not qualitative, which indicates that both teams are faced with difficulties because of the regulation of cognition as a cognitive process of superior level. Girls in relation to boys in the total of the sample use more often the strategies of regulation of cognition and not of the knowledge of cognition.