This research reports on findings from a large-scale study amongst Australian high school students investigating the need to distinguish between academic motivation for mathematics, English and science subjects (with an additional focus on gender and year-level differences). This paper utilises the Student Motivation and Engagement Wheel (Martin, 2003) as a basis for conceptualising academic motivation and engagement and the Student Motivation and Engagement Scale (SMES - Martin, 2001, 2002) as a basis for measuring it. A total of 1,801 students from six government high schools were administered the Student Motivation and Engagement Scale. Confirmatory factor analysis (CFA) provided support for the domain specificity of motivation and engagement across three distinct high school subject areas. Additional analyses utilising multiple-indicator-multiple-cause (MIMIC) modelling identified a general trend that girls are more motivated across subjects than boys. The few significant interactions broadly showed that as girls move into middle high school they are more motivated than boys in mathematics and less motivated in science and English. Implications for pedagogy and further research are discussed.