Nanorods based on ZnO for surface enhanced Raman spectroscopy are promising for the non-invasive and rapid detection of biomarkers and diagnosis of disease. However, optimization of nanorod and coating parameters is essential to their practical application. With the goal of establishing a baseline for early detection in biological applications, gold-coated ZnO nanorods were grown and coated to form porous structures. Prior to gold deposition, the grown nanorods were 30-50 nm in diameter and 500-600 nm in length. Gold coatings were grown on the nanorod structure to a series of thicknesses between 100 and 300 nm. A gold coating of 200 nm was found to optimize the Rhodamine B model analyte signal, while performance for rat urine depended on the biomarkers to be detected. These results establish design guidelines for future use of Au-ZnO nanorods in the study and early diagnosis of inflammatory diseases.