Gastrointestinal disease is the number one killer of horses. Little is known about the maintenance of microbes in the equine hindgut and how to distinguish a healthy gut in a live horse. Utilization of internal and external digestibility markers and starch fermentation has been extensively studied in ruminants and is the basis for research conducted on horses. The aims of this study were to investigate the effects of two equine feed digestive aid supplements on hindgut health (HGH) as reflected in fecal pH and digestibility and to compare and validate DM digestibility measurements through the use of internal and external markers such as chromium oxide (CR), lignin (Lig), indigestible ADF (iADF), indigestible NDF (iNDF), and indigestible lignin (iLig). Nine mature Quarter horses (six geldings, three mares) were used in a crossover design, three feeding periods of 17 d (51 d total), using three treatments: control, no feed additive (CON), Smartpak (SP; Plymouth, MA), or Platinum Performance (PP; Buellton, CA). Both SP and PP contained a strain of Lactobacillus, whereas SP further supplied mannanoligosaccharides (MOS) and fructooligosaccharides (FOS) and PP supplied Saccharomyces boulardii. Within the 17-d period, horses were offered orchard grass hay and sweet cob grain and the assigned treatment daily and four CR cookies to deliver 8 g/d of CR for the last 7 d of each period. Total feces were collected from 15 to 17 d. Feed and fecal samples were dried, ground, and sent to ANALAB (Fulton, IL) for nutrient analysis. Duplicate samples of feed and feces were placed in ruminally cannulated cows for in situ determination of iADF, iNDF, and iLig to estimate digestibility. Estimated CR fecal output, CR DMI, and DM digestibilities were evaluated using the root mean square prediction error percentage of the observed mean (RMSPE), concordance correlation coefficient (CCC), and Nash–Sutcliffe efficiency methods. Marker predictive ability tests showed iADF to have the least amount of bias with the smallest RMSPE (4%), largest CCC (0.43), and the largest amount of random bias (error of dispersion = 0.45). Supplementation of PP decreased CR DM digestibility (P < 0.02). Smartpak increased fecal pH (P < 0.09), but PP had no effect on fecal pH. Therefore, SP had a beneficial effect on HGH that is believed to be due to MOS and FOS.