Nationally, health risks from communicable diseases in schools are drawing renewed attention as routine childhood vaccination coverage declines. These risks are not uniform: schools differ in physical environment, resources, and student behavior. While lessons from the COVID pandemic may provide insight into how such differences create inequalities, little existing evidence documents (or refutes) school COVID risk disparities. This paper begins to fill this gap by examining racial disparities in two factors affecting risk: vaccination rates and indoor density (classroom space per pupil) of New York City elementary schools (then examining middle and high schools separately). We explore the link between school COVID risk and absenteeism as well as racial disparities both within and between neighborhoods. While Asian and White students, on average, attend schools with higher vaccination rates, they also face more crowded classrooms than Black or Hispanic students. White students are more likely than Black students to attend schools with indoor density above and vaccination rates below expert recommended critical thresholds. Roughly half of the racial disparity in school COVID risk reflect differences across neighborhoods rather than within them. Controlling for school COVID risk narrows racial gaps in attendance rates and chronic absenteeism by roughly one-third to one-half. Results are similar for the middle and high schools. Our findings highlight the importance of health risks in schools, distinguishing between those rooted in physical environments and those driven by collective behavior.