Plasma ceramide levels (henceforth, "ceramides") are biomarkers of some diseases that are comorbidities of Down syndrome (DS). We sought to determine if comorbidities in DS were associated with ceramides, studying a convenience cohort of 35 study participants, all ≥12 months old. To identify comorbidities, we reviewed the problem lists in electronic health records that were concurrent with sample collection. We placed clinically related comorbidities into one of five categories of comorbidities, henceforth, categories: obesity/overweight; autoimmune disease; congenital heart disease; bacterial infection; and central nervous system (CNS) condition. We measured the eight ceramides most frequently associated with disease using liquid chromatography-tandem mass spectrometry. We calculated a ceramide composite outcome score (CCOS) for each participant by normalizing each ceramide level to the mean for that level in the study population and then summing the normalized levels, to be proxy variable for all eight ceramides in aggregate. We used multivariable linear regression models adjusted for age and sex to test associations of categories with ceramides and with CCOSs. Post hoc, we realized that co-occurring comorbidities might interfere with establishing associations between predictor categories and ceramides and that stratified analyses might eliminate their influence on associations. We posited that CCOSs could be used to screen for associations of categories with multiple ceramides, since most diseases have been associated with more than one ceramide. We chose to omit in the stratified analyses the two categories that were the most different from one another in their associations with their CCOSs, having the most divergent regression coefficients (the highest positive and lowest negative coefficients). We first omitted one of these two divergent categories in a stratified analysis and tested in the remaining participants (those without a comorbidity in the interfering category) for associations of the other four categories with their CCOSs and then did the same for the other divergent category. In each of these two screening stratified analyses, we found one category was significantly associated with its CCOS. In the two identified categories, we then tested for associations with each of the eight ceramides, using the appropriate stratified analysis. Next, we sought to determine if the associations of the two categories with ceramides we found by omitting participants in the interfering categories held in our small sample for participants in the omitted categories as well. For each of the two categories, we therefore omitted participants without the interfering category and determined associations between the predictor category and individual ceramides in the remaining participants (those with a comorbidity in the interfering category). In the a priori analyses, autoimmune disease was inversely associated with C16 and CNS condition was inversely associated with C23. Obesity/overweight and CNS condition were the two categories with the most divergent regression coefficients (0.037 vs. -0.048). In post hoc stratified analyses, after omitting participants with obesity/overweight, thereby leaving participants without obesity/overweight, bacterial infection was associated with its CCOS and then with C14, C20, and C22. However, in the companion stratified analyses, omitting participants without obesity/overweight, thereby leaving participants with obesity/overweight, bacterial infection was not associated with any of the eight ceramides. Similarly, in post hoc stratified analyses after omitting participants with a CNS condition, thereby leaving participants without a CNS condition, obesity/overweight was associated with its CCOS and then with C14, C23, and C24. In the companion analyses, omitting participants without a CNS condition, thereby leaving participants with a CNS condition, obesity/overweight was inversely associated with C24.1. In conclusion, CNS and autoimmune disease were inversely associated with one ceramide each in a priori analyses. In post hoc analyses, we serendipitously omitted categories that interfered with associations of other categories with ceramides in stratified analyses. We found that bacterial infection was associated with three ceramides in participants without obesity/overweight and that obesity/overweight was associated with three ceramides in participants without a CNS condition. We therefore identified obesity/overweight and CNS conditions as potential confounders or effect modifiers for these associations. This is the first report of ceramides in DS and in human bacterial infection. Further study of ceramides in comorbidities of DS is justified.