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This paper explores the use of HLM analysis in determining the implementation effects of two science curriculum units on student learning. It also compares HLM results with prior results from ANCOVA analyses. HLM analyses were considered as an alternative to ANCOVA because student data were nested within classrooms. The data for this study are from the Scaling-up Curriculum for Achievement, Learning and Equity Project (SCALE-uP). The sample consists of Grade 6 and Grade 7 students from five matched pairs of middle schools in a large, diverse, metropolitan school district in the US. The HLM null model indicates that approximately 15% of the total variance in student gain scores was found between classrooms. Curriculum treated as a classroom factor was significant for both units tested, as was also the case when treated at the individual level in ANCOVA. However, there were large differences in the effect sizes reported by the two analysis techniques. A major implication is that when the students are nested in classrooms and schools, researchers should consider multi-level analysis and account for classroom/school contexts.