There is increasing concern about risky behaviors and poor mental health among school-aged youth. A critical factor in youth well-being is school attendance. This study evaluates how school organization and structure affect health outcomes by examining the impacts of a popular urban high school reform -- “small schools” -- on youth risky behaviors and mental health, using data from New York City. To estimate a causal estimate of attending small versus large high schools, we use a two-sample-instrumental-variable approach with the distance between student residence and school as the instrument for school enrollment. We consider two types of small schools – “old small schools,” which opened prior to a system-wide 2003 reform aimed at increasing educational achievement and “new small schools,” which opened in the wake of that reform. We find that girls enrolled in older small schools are less likely to become pregnant, and boys are less likely to be diagnosed with mental health disorders than their counterparts in large schools. Both girls and boys enrolled in more recently opened small schools, however, are more likely to be diagnosed with violence-associated injuries and (for girls only) with mental health disorders. These disparate results suggest that improving a school’s organization and inputs together is likely more effective in addressing youth risky behaviors than simply reducing school size.