Background: While crime and violence in schools are derived primarily from factors external to schools, violent behavior may also be aggravated by factors in the school environment, including the physical environment, its educational and social climate, and its organizational capacity and composition. The objective of this study is to examine the effect of the school's organizational and educational environment on crime rates in secondary schools and to examine how neighborhood factors influence these relationships. Methods: School and neighborhood crime rates for 95 middle (MS) and high (HS) schools were calculated using data from the Los Angeles Unified School District (LAUSD) Police Department and Los Angeles Police Department, respectively. School-level organizational and educational variables, including the academic performance index (API), were obtained from the California Department of Education. A measure of neighborhood dilapidation was created using variables collected on a neighborhood environmental survey. Linear regression was used to examine the relationship between organizational and educational school variables and school crime rates. Community crime and dilapidation were added to the model to examine the influence of the school-community context relationships. Results: HS had higher crime rates than MS. As the percentage of certified teachers and student to staff ratios increased, school crime decreased (p less than 0.01). An API of below basic performance was significantly associated with increasing school crime rates (p less than 0.05). Neighborhood crime was not significantly associated with school crime, although dilapidation was positively and significantly associated with school crime even after controlling for community crime (p less than 0.05). Conclusions: Both school- and neighborhood-level factors were associated with increasing crime rates in secondary schools. School violence prevention efforts should include school and community partnerships to address these potentially modifiable factors. (Contains 3 tables.)