The ability to measure environmental contaminants in biological tissues and fluids is important in the characterization of exposure. However, the analysis of certain contaminants in these matrices presents significant challenges. Perchlorate (ClO4-) has emerged as a potential contaminant of concern primarily in drinking water and also in contaminated food. Significant advances have been made in the analysis of perchlorate in environmental matrices (water, soil) by ion chromatography (IC). In contrast, the analysis of perchlorate in extracts of biological tissues and fluids (vegetation, organs, milk, blood, urine, etc.) presents several challenges including small sample sizes, extracts with high matrix conductivity, and co-elution of other ions during IC analysis. To be able to detect low concentrations of perchlorate in biological samples, interferences must be removed or minimized, such as through the use of preparative chromatography cleanup techniques and/or alternative analytical methods less susceptible to common interferences (preconcentration or mass spectrometric detection). We present discussion and examples of the challenges encountered in the analysis of tissue extracts and fluids for perchlorate by IC and how some of those analytical challenges have been overcome.