We present a Fourier-domain, multiplexed low coherence interferometry (LCI) instrument designed for application to intravaginal measurement of microbicidal gel distribution. Microbicide gels are topical products developed to combat sexually transmitted diseases, such as HIV/AIDS, by acting as delivery vehicles for active drugs and barrier layers to vaginal tissue. Measuring microbicide gel vaginal distribution is key to understanding the gel's biological effectiveness. This study presents a new LCI system for measuring gel distribution that uses six multiplexed channels to achieve broad area scanning without the need for a mechanical scanner. The presented results characterize the performance of the Fourier-domain multiplexed LCI system in measuring gel thickness distribution. The system demonstrates good optical signal-to-noise ratio, steady performance across all channels, negligible cross talk, and accurate measurement with micrometer scale resolution. The potential impact of using a multiplexed LCI system for in vivo measurements is also discussed.