smORF encoded polypeptides (SEPs) are difficult to predict due to their small size. While modern genome annotation tools are capable of identifying smORFs, their reliability is often uncertain. Furthermore, experimental validation of smORFs has primarily focused on a limited set of model organisms. Here we conduct a comprehensive analysis of annotated smORFs in a diverse range of bacteria interacting with eukaryotic hosts. Our analysis revealed that bacterial genomes typically harbor between 100 and 300 annotated smORFs, predominantly encoding SEPs exceeding 40 residues and annotated as hypothetical proteins. We show that functional annotation of SEPs can be improved to some extent with the currently available resources, and that SEPs exhibit distinct functional profiles in bacteria associated with different host types (plant vs. animal). We also found that most of the experimentally validated SEPs are conserved, and that all the annotated SEPs begin with methionine, while that is not always the case for the experimentally validated ones. Our findings underscore the need for improved annotation methods and further experimental characterization to fully understand the functional roles and evolutionary significance of smORFs in bacteria-host interactions.