Language learning is multifaceted, and within Second Language Acquisition (SLA) research, motivation is one of the most frequently studied aspects. The impetus of the current study is to further explore second language learning motivation as well as its impact on the language acquisition process within the context of Content and Language Integrated Learning (CLIL). This study uses Dörnyei’s (2009) framework of the L2 Motivational Self System from which the Motivational Factors Questionnaire (MFQ) has been created and validated by Ryan (2009). This study was conducted at the high school level in Sweden and includes students enrolled in CLIL programs (N = 109) and non-CLIL programs (N = 68) at three different schools. In this paper, the subcategories of the MFQ are analyzed using one-way ANOVAs with CLIL/non-CLIL, L1, and gender as the independent variables. The results indicate that there are differences in attitudes and motivation of CLIL vs. non-CLIL students.