Citrus tristeza virus (CTV) (genus Closterovirus) is a plant pathogen which infects economically important citrus crops, resulting in devastating crop losses worldwide. In this study, we analyzed leaf metabolite extracts from six sweet orange varieties and a mandarin × tangor cross infected with CTV collected at the Lindcove Research and Extension Center (LREC; Exeter, CA). In order to analyze low volatility small molecules, the extracts of leaf metabolites were derivatized by N-methyl-N-trimethylsilyl-trifluoracetamide (MSTFA). Chemical analysis was performed with gas chromatography/mass spectrometry (GC/MS) to assess metabolite changes induced by CTV infection. Principal Component Analysis (PCA) and Hotelling’s T2 were used to identify outliers within the set of samples. Partial Least Square Discriminant Analysis (PLS-DA) was applied as a regression method. A cross-validation strategy was repeated 300 times to minimize possible bias in the model selection. Afterwards, a representative model was built with a sensitivity of 0.66 and a specificity of 0.71. The metabolites which had the strongest contribution to differentiate between healthy and CTV-infected were found to be mostly saccharides and their derivatives such as inositol, d-fructose, glucaric and quinic acid. These metabolites are known to be endogenously produced by plants, possess important biological functions and often found to be differentially regulated in disease states, maturation processes, and metabolic responses. Based on the information found in this study, a method may be available that can identify CTV infected plants for removal and halt the spread of the virus.