This study demonstrates the continued existence of gender disparity with respect to salary in four neurologic specialties in the largest public healthcare system of the Western United States without the bias of self-report. We extracted physician salary information from the publicly available UC pay system database and obtained Scopus (http://www.scopus.com/home.url) and Web of Science publication counts and h-indices via searching individual faculty by name and specialty. Faculty gender, institution, specialty, ranking, chairmanship, degrees, and salary data were collected through review of departmental websites and individual faculty profiles. All faculty members (n = 433) from the departments of ophthalmology, otolaryngology, neurosurgery and neurology in the UC pay system database in 2008 were selected for analysis. We found that female faculty members in the 2008 UC healthcare system were significantly underrepresented from the highest salary brackets, representing only 12.5 and 2.6 % of those earning $300,001-$400,000 and over $400,000, respectively (p < 0.01). The female-to-male salary ratio in 2008 for all UC physicians earning over $100,000 was 0.698 (p < 0.00001). Multivariate regression modeling demonstrated a 12 % salary deficit (95 % CI 2-21 %, p = 0.02) for women in the UC healthcare system after controlling for institution, professorial rank, chairmanship, specialty, Scopus publication count, and Scopus h-index. Despite recent efforts at educational equality in the training of physicians, gender disparities still persist within academic medicine.