Germ-free (GF) mice are entirely devoid of all microorganisms. GF mice are one of the most powerful tools for studying the role of the microbiome in a phenotype and moving the microbiome field from association to causation. They allow the introduction of specific microbes or microbial communities to interrogate the causality of microbiomes in protecting against or contributing to a phenotype. Here, we report critical and underappreciated challenges in using GF models to investigate intergenerational effects of maternal diet and microbiota on offspring health.