A recent disease prevalence study of the largest documented Down syndrome (DS) cohort in the United States strongly suggested significant disparity in general infectious disease conditions among individuals with DS versus those without DS. In this follow-up retrospective analysis, we explored these differences in greater detail by calculating prevalence of 52 infectious diseases, across 28 years of data among 6078 individuals with DS and 30,326 age- and sex-matched controls, abstracted from electronic medical records within a large Midwestern health system. We found that the DS cohort had higher prevalence of pneumonias (including aspiration, viral, bacterial, pneumococcal, and unspecified/atypical); otitis externa; and the skin infections impetigo, abscess, and cellulitis. To the contrary, the DS cohort had lower prevalence of many respiratory infections other than pneumonia (including influenza, strep pharyngitis, upper respiratory infection, sinusitis, tonsillitis, laryngitis, bronchitis, scarlet fever, and otitis media); sexually transmitted infections (including bacterial vaginosis, chlamydia, genital herpes, HIV/AIDS, human papillomavirus, pelvic inflammatory disease, and trichomoniasis); mononucleosis; shingles; unspecified hepatitis; intestinal infections; and enteritis. These findings highlight that individuals with DS could be more or less prone to different infectious diseases than their non-DS matched counterparts. Additional research to understand why these differences exist and how they might affect the clinical approach to patients with DS is warranted.