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To protect their health, children need to understand infectious diseases—how we get them, what they do to us, how to avoid them. Much research on children’s understandings of illness has been guided by Piagetian theory and has assessed the structural complexity of children’s thinking about disease, independent its factual correctness (Bibace & Walsh, 1980; Perrin & Gerrity, 1981). More recent work has been guided by an intuitive or naïve theories perspective (Wellman & Gelman, 1998) and has examined the content of children’s thinking, particularly their grasp of a germ or virus as the causal agent (e.g., Au et al., 2008; Au & Romo, 1996; Kalish, 1996). The present study seeks to integrate the assessment of structure and content and advance the intuitive theories perspective by assessing children’s understanding of a causal chain from risk behavior to internalization of a disease agent to the emergence of disease symptoms. The methodology, derived in part from concept mapping (Novak, 2005; and see Jones & Rua, 2008; Davies et al., 2004), assesses the three key qualities of intuitive theories highlighted by Wellman and Gelman: causal explanatory framework, ontology, and logical coherence. We predicted developmental differences in intuitive theories of flu in terms of mastery of key theoretical propositions linking risk behaviors to symptoms, use of a relevant biological ontology, and logical connectedness of thought. Demographic and experiential predictors of these summary measures were also examined. Participants were 156 students in grades three, five, and seven who completed focused open-ended interviews about causal processes in flu; 35.4% were European-American, 58.9% were Hispanic, primarily Mexican-American, and 5.7% were other minorities. A theoretical propositions score consisted of the proportion of eight propositions mastered; a biological ontology score represented the number of five disease-relevant biological terms used (e.g., germ, virus, immune); and a logical coherence score assessed making explicit connections among risk behavior, disease agent, and symptom. Level of Piagetian complexity of understanding was also coded for comparison. Codings were done reliably by trained pairs of coders. Scores on all measures increased with age, with third graders typically setting forth less sophisticated theories than older children did and having more difficulty describing internal processes linking exposure to an infected person to flu symptoms. Even older children typically lacked awareness of the immune system’s role in flu. The average correlation among the four summary measures was .48 (range .28 to .58), suggesting that the structural complexity and accuracy of explanations are distinct but positively interrelated. In multiple regression analyses, the four summary scores were all predicted significantly by age. Theoretical proposition score was also predicted by not participating in the free lunch program, having a more educated parent, and, with these SES-related indices controlled, Hispanic/minority ethnicity, which also predicted higher ontology and Piagetian complexity scores. Gender and experience with flu had no bearing. The analytic approach developed for this study captures the key qualities of intuitive theories of infectious disease and illuminates the development of both the structure and content of children’s thinking about it.