Abstract Background Colorectal cancer is a heterogeneous disease arising from at least two precursors—the conventional adenoma (CA) and the serrated polyp. We and others have previously shown a relationship between the human gut microbiota and colorectal cancer; however, its relationship to the different early precursors of colorectal cancer is understudied. We tested, for the first time, the relationship of the gut microbiota to specific colorectal polyp types. Results Gut microbiota were assessed in 540 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples. Participants were categorized as CA cases ( n = 144), serrated polyp cases ( n = 73), or polyp-free controls ( n = 323). CA cases were further classified as proximal ( n = 87) or distal ( n = 55) and as non-advanced ( n = 121) or advanced ( n = 22). Serrated polyp cases were further classified as hyperplastic polyp (HP; n = 40) or sessile serrated adenoma (SSA; n = 33). We compared gut microbiota diversity, overall composition, and normalized taxon abundance among these groups. CA cases had lower species richness in stool than controls ( p = 0.03); in particular, this association was strongest for advanced CA cases ( p = 0.004). In relation to overall microbiota composition, only distal or advanced CA cases differed significantly from controls ( p = 0.02 and p = 0.002). In taxon-based analysis, stool of CA cases was depleted in a network of Clostridia operational taxonomic units from families Ruminococcaceae , Clostridiaceae , and Lachnospiraceae , and enriched in the classes Bacilli and Gammaproteobacteria , order Enterobacteriales , and genera Actinomyces and Streptococcus (all q