Measles is a very contagious disease that is the leading cause of death of children. Traditionally, the measles virus (MV) can be detected using qRT-PCR, ELISA, and IFA assays. However, these techniques often provide inconclusive information and do not allow for low-level detection. Since, viral shedding of an infected person can be from 1 to 10,000 pfu, it is important to attain an assay capable of low level MV detection. Surface-enhanced Raman spectroscopy (SERS) demonstrates a quick, label-free spectroscopic method for detection of low levels of molecular samples. In this study, SERS- Ag nanorods assays were used with the Partial Least Squares-Discriminant Analysis (PLS-DA) chemometric method to classify D4, A, and H1 measles genotypes with 100% sensitivity and specificity. Additionally, the SERS assay was combined with Partial Least Squares (PLS) to accurately (RMSECV=0.024) estimate low molecular concentrations (103 -10 pfu/ml) of MV samples with high linearity (R2=0.99).