Clinical chemistry analysis of body fluids from non-blood or urine sources presents a technical challenge for clinical laboratories. Examples of body fluids include biliary secretions, cerebrospinal fluid, cyst contents, dialysate, gastric aspirates, peritoneal fluid, pleural fluid, stool, surgical drain fluid, synovial fluid, and wound exudates. The heterogeneous nature of these body fluids presents technical difficulties for analysis. For example, body fluid specimens may have presence of hemolysis, icterus, or lipemia (‘interference indices’) that can interfere with clinical chemistry analysis. In the related research article, we analyzed the distribution of these interference indices and body fluid samples submitted for analysis at an academic medical center central clinical laboratory and compared this to data from serum/plasma specimens. The data in this article provide the body fluid type, clinical chemistry testing ordered, interference indices, and whether the indices exceeded the manufacturer's recommendations in the package insert for serum/blood specimens. The analyzed data are provided in the supplementary tables included in this article. The dataset reported is related to the research article entitled “Review of interference indices in body fluids specimens admitted for clinical chemistry analyses” [1].