Objectives: Reported pertussis incidence has increased markedly in recent years. In addition to the documented increase in under-immunization and waning immunity, the increase may be related to the more frequent use of child care services by parents over the last few decades. Additionally, clustering of outbreaks may be related to neighborhood characteristics not previously identified. Study Design: We conducted a citywide case-control study of children in Philadelphia aged birth through six years, between 2001 and 2013. Cases were reported as probable pertussis diagnoses to the Health Department. Controls were sampled from the city's immunization information system and matched to the cases by date of birth. Methods: Multilevel logistic regression was used to isolate the independent contributions of individual and neighborhood risk factors and the corresponding relative odds of pertussis. The density of day cares in each neighborhood served as the main exposure and reported incident cases of confirmed and probable pertussis was the main outcome. Results: Between 2001 and 2013, 410 cases of confirmed and probable pertussis were included with four controls matched per case yielding a final sample of 2050 children from 45 Philadelphia neighborhoods. There was a 30% increase in the risk of pertussis based solely on the neighborhood where the children resided (median odds ratio 1.3, 95% credible interval 1.1, 1.6). The density of day cares in each neighborhood was unrelated to the distribution of pertussis cases. Conclusions: Pertussis clustering was observed at the neighborhood level in Philadelphia, but was unrelated to the neighborhood's day care density. From a Health Department perspective, the highest risk neighborhoods should be targeted for vaccine campaigns and further research to identify the etiologic risk factors. (author abstract)