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Introduction: One-fifth to one-third of students in high-poverty, urban school districts do not attend school regularly (missing ≥6 days per year). Health related fitness is shown to be associated with absenteeism, although this relationship may differ across poverty and gender subgroups.Hypothesis: We hypothesized that area poverty would be a stronger effect modifier on the association of fitness (cardiorespiratory, muscular endurance, and muscular strength fitness composite percentile scores) and subsequent absenteeism (one-year lagged days absent) in girls compared with boys.Methods: Six cohorts of New York City public school students were followed from grades 5-8 during 2006/7-2012/13 (n=349,381). Stratified three-level longitudinal generalized linear mixed models were used to test the modification of poverty on the association of fitness changes and one-year lagged child-specific days absent across gender.Results: The fitness-absenteeism association was not significant in boys attending schools in high/very high (p=0.075) or low/mid poverty (p=0.454) areas. In girls attending schools in high/very high poverty areas, greater improvements in fitness the prior year were associated with greater improvements in attendance (p=0.034). Relative to the reference group (>20% decrease in fitness composite percentile scores from the prior year), girls with a large increase in fitness (>20%) demonstrated 10.3% fewer days absent (IRR 95% CI: 0.834, 0.964), followed by those who had a 10-20% increase in fitness (9.2%, IRR 95% CI: 0.835, 0.987), no change (5.4%, IRR 95% CI: 0.887, 1.007) and a 10-20% decrease in fitness (3.8%, IRR 95% CI: 0.885, 1.045). In girls attending schools in low/mid poverty areas, the fitness-attendance relationship was also positive, but no clear trend emerged.Conclusions: Fitness improvements may be more important to attendance improvements in high/very high poverty girls compared with low/mid poverty girls, and both high/very high and low/mid poverty boys. In conclusion, expanding school-based physical activity programs for girls in high-poverty neighborhoods may increase student attendance.