Objectives:The article aims to give Spectrum/estimation and projection package (EPP) users and the scientific community a basic understanding of the underlying statistical model used to incorporate hierarchical structure in HIV subnational estimation, and to show how it has been implemented in the Spectrum/EPP interface for improving subepidemic estimation. The article also provides recommended default settings for this new model.Methods:We apply a generalized linear mixed-effects model on antenatal clinics prevalence data to get area-specific prevalence and uncertainty estimates, and transform those estimates to auxiliary data. We then fit the EPP model to both the observed data and auxiliary data.Results:We apply the proposed methods to four countries with different levels of data availability. We compare the out-of-sample prediction accuracy of the proposed method with varying auxiliary sample sizes and EPP without auxiliary data.Conclusion:We find that borrowing information from data-rich areas to data-sparse areas using our proposed method improves EPP fit in data-sparse areas. We recommend using the sample size estimated from generalized linear mixed-effects model as the default auxiliary sample size. Copyright (C) 2017 Wolters Kluwer Health, Inc. All rights reserved.