Background: The Inventory of Statements About Self-Injury (ISAS) is a psychometrically valid tool to evaluate the motives of non-suicidal self-injury (NSSI), but there is a lack of investigations which could test gender differences in the factor structure of the measurement. However, several differences across gender were identified in self-harm (e.g., in prevalence, methods, functions). Therefore, our study focused on further analyses of the dimensionality of the ISAS functions. Methods: On a Hungarian adolescent sample (N=1015; 66.1% girl; mean age was 16.81, SD=1.42; 41.2% had a history of NSSI) confirmatory factor analysis and exploratory structural equation modeling frameworks were used to test the factor structure of the ISAS part II. Results: Results support the two-factor structure of the questionnaire. Intrapersonal and interpersonal motivation factors emerged in the whole sample, but this factor structure varied across gender. Furthermore, among girls, intrapersonal motivation of NSSI associated with higher loneliness, more inflexible emotion regulation, as well as more pronounced level of internalizing and externalizing mental illness symptoms. Conclusions: Our findings are sufficiently strong arguments to the need of separate examination of NSSI functionality among adolescent girls and boys. It can be assumed that there is a gender difference in the motives underlying in NSSI. In addition, precise scanning of patterns of NSSI functions may further help us to identify the most at-risk adolescents regarding self-harm.