Multilevel, multivariate models examined the relationship between Primary Care Medical Home (PCMH) practice systems as measured by the Physician Practice Connections(R)-Readiness Survey (PPC(R)-RS) and costs (total, outpatient, and inpatient) using 2008 patient data from 21 primary care clinics. Overall, PPC-RS scores were associated with insignificant changes in total (-$75/person, 1.1%) outpatient (-$67/person, 1.2%), and inpatient ($68/person, 0.5%) costs. However, improved PPC-RS scores were associated with significant decreases in total ($2378, 4.4%) and outpatient ($1282/person, 3.5%) costs among patients with 11 or more prescriptions suggesting higher functioning PCMHs may lead to reduced costs among the most complex and costly patients.