Background: This study used a new Crime Prevention Through Environmental Design (CPTED) assessment tool to test the associations between physical attributes of schools and violence-related behaviors and perceptions of students. Methods: Data were collected from 4717 students from 50 middle schools. Student perceptions of risk and safety, and violence were assessed. Evaluators used the CPTED School Assessment (CSA) to quantify how well the physical elements of each school correspond to ideal CPTED principles. Generalized linear mixed models were used to adjust for school- and student-level characteristics. Results: Higher CSA scores were generally associated with higher perceptions of safety and lower levels of violence perpetration and perceived risk in unadjusted models. Higher CSA scores were also associated with lower odds of missing school because of safety concerns in most adjusted models, with significant adjusted odds ratios (AORs) ranging from 0.32 to 0.63. CSA scores for parking and bus loading areas also remained associated with higher perceived safety (AORs = 1.28 and 1.32, respectively) and lower perceived risk (AORs = 0.73 and 0.66, respectively) in adjusted models. Conclusions: The CSA is useful for assessing school environments that are associated with violence-related behaviors and perceptions. The CSA might help guide school environmental modifications to reduce violence.