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A debate exists between the merits of direct versus inquiry instruction. Direct instruction supports accelerated student learning, whereas inquiry activities can be perceived as more motivating and interesting to students (Assor, Kaplan, Kanat-Maymon, & Roth, 2005; Kirschner, Sweller, & Clark, 2006). This study investigated how variation in the sequence of science instruction for middle-school students, using direct and inquiry methods influenced achievement scores and motivational variables such as perceived autonomy, competence, and interest. Overall, greater interest was reported during inquiry instruction, compared to either direct instruction or a scripted lab. No significant differences in achievement were observed when comparing direct to inquiry methods. Perceived autonomy and competence were equal across all sequences. Recommendations for practice and implementation are suggested.