Pre-algebra mathematical competencies were assessed for a large and diverse sample of sixth graders (n = 1,926), including whole number and fractions arithmetic, conceptual understanding of equality and fractions magnitudes, and the fractions number line. The goal was to determine if there were clusters of students with similar patterns of pre-algebra strengths and weaknesses and if variation between clusters was related to mathematics attitudes, anxiety, or for a subsample (n = 342) some combination of intelligence, working memory, or spatial abilities. Critically, strengths and weaknesses were not uniform across the three identified clusters. Lower-performing students had pronounced deficits in their understanding of mathematical equality, fractions magnitudes, and the fractions number line. Higher-performing students had particular advantages in whole number and fractions arithmetic, and the fractions number line. Students could be reliably placed into clusters based on their mathematics self-efficacy and a combination of intelligence and spatial abilities. The results contribute to our understanding of key aspects of students' mathematical development, highlight areas in need of intervention for at-risk students, and identify cognitive areas in which scaffolds might be incorporated into these interventions.