Detailed guidebooks for each HSIS State are available to HSIS users. The purpose of the guidebooks is to provide sufficient information for both the analyst and the programmer to effectively use the system. The guidebooks document data quality issues uncovered through annual quality control checks or reported by system users.

The guidebook for each State contains a basic description of the State data system, an alphabetized listing (by file type) of all available variables, detailed definitions of each category present within each variable, and notes on the quality of the variable. The guidebooks are updated on a two-three year cycle or as significant changes occur. (Note that in the past, HSIS also published a “Volume II” containing single-variable tabulations for a large number of "key" variables within each of the files across five years. Based on a user survey, Volume II is no longer published. However, for users needing information on sample sizes across years, custom-designed tables will be prepared by HSIS staff on request.)