Accurate immunoassay results depend not only on assay design but critically on sample preparation. This chapter explores analyte-specific processing strategies for stool samples in both qualitative and quantitative immunoassays, highlighting challenges in gastrointestinal infection diagnostics, inflammatory bowel disease, and colorectal cancer screening. It emphasizes the role of dilution buffers in minimizing interference, stabilizing analytes, and ensuring reproducibility. Practical examples illustrate how buffer composition and sample handling impact diagnostic accuracy. The chapter underscores that tailored sample preparation is essential for reliable immunoassay performance, especially in complex matrices like stool.