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Introduction: Environmental exposure to indoor dust is known to be associated with myriad health conditions, especially among children. Established routes of exposure include inhalation and non-dietary ingestion, which result in the direct exposure of gastrointestinal epithelia to indoor dust. Despite this, little prior research is available on the impacts of indoor dust on the health of human gastrointestinal tissue. Methods: Cultured human colonic (CCD841) cells were exposed for 24 h to standard trace metal dust (TMD) and organic contaminant dust (OD) samples at the following concentrations: 0, 10, 25, 50, 75, 100, 250, and 500 µg/mL. Cell viability was assessed using an MTT assay and protease analysis (glycyl-phenylalanyl-aminofluorocoumarin (GF-AFC)); cytotoxicity was assessed with a lactate dehydrogenase release assay, and apoptosis was assessed using a Caspase-Glo 3/7 activation assay. Results: TMD and OD decreased cellular metabolic and protease activity and increased apoptosis and biomarkers of cell membrane damage (LDH) in CCD841 human colonic epithelial cells. Patterns appeared to be, in general, dose-dependent, with the highest TMD and OD exposures associated with the largest increases in apoptosis and LDH, as well as with the largest decrements in metabolic and protease activities. Conclusions: TMD and OD exposure were associated with markers of reduced viability and increased cytotoxicity and apoptosis in human colonic cells. These findings add important information to the understanding of the physiologic effects of indoor dust exposure on human health. The doses used in our study represent a range of potential exposure levels, and the effects observed at the higher doses may not necessarily occur under typical exposure conditions. The effects of long-term, low-dose exposure to indoor dust are still not fully understood and warrant further investigation. Future research should explore these physiological mechanisms to further our understanding and inform public health interventions.