Home stool collection enables large-scale sampling for companion animal microbiome studies. We’ve tailored human stool sample collection kits to be suitable for collection from cats and dogs (e.g., to include materials helpful for collection from litter boxes for cat stool). Kit contents include stool collection tubes, a biospecimen bag, plastic scoop, nitrile gloves, empty plastic bag, and sticker to indicate desired size of sample, and a pet questionnaire. Kits can be provided by a recruiting clinician during routine veterinarian visits or shipped directly to the participant’s home, depending the study’s needs.