Citrus tristeza virus (CTV) (genus Closterovirus) is a plant pathogen which infects economically important citrus crops such as sweet oranges, mandarins, limes and grapefruit varietals. Within the last 70 years, an estimated 100 million citrus trees have been destroyed due to CTV infection worldwide. Present measures to contain CTV infection include scouts for visual assessment, and molecular analysis methods such as enzyme linked immunosorbent assay and reverse transcription polymerase chain reaction. Volatile organic compound (VOC) profiling may offer an alternative method of disease detection. In this study, we used a “Twister™” sorbent system for in-field VOC sampling. Chemical analysis was performed with thermal desorption gas chromatography time-of-flight mass spectrometry, and data were subjected to unsupervised and supervised analysis. Samples were collected from healthy trees, those with asymptomatic CTV, and those with CTV that were coinfected with a secondary unrelated bacterial infection of Spiroplasma citri, the causal agent of citrus stubborn disease (Stubborn). A total of 383 VOCs were detected across three classes: healthy control trees, CTV infected, and CTV coinfected with Stubborn. Mathematical models of this data were built to successfully differentiate: (a) healthy trees from CTV infected trees; (b) healthy trees from both CTV and CTV coinfected with Stubborn; and (c) to effectively differentiate between healthy trees and CTV infected trees, without consideration of Stubborn coinfection (the model would work on both singly or coinfected trees). The putative CTV biomarkers observed were terpenoid based (myrcene, carene, ocimene, bulnesene), two alcohols (n-undecanol, surfynol) and two acetones (geranyl acetone and neryl acetate).