Context: Parkinson’s disease (PD) is catalogued as a disorder that causes motor symptoms; the evidence of literature shows the PD starts with non-motor signs, which can be detected in prodromal phases. These previous phases can be analyzed and studied through magnetic resonance images (MRI), electroencephalography (EEG) and microbiome.Objective: To systematically review the areas of the brain and brain-gut axis which affect in early Parkinson’s disease that can possibly be visualized and analyzed by MRI, EEG and the microbiome.Evidence acquisition: Pubmed and Embase databases were used until July 30, 2018 as to search for early Parkinson’s disease at its earliest non-motor symptoms stage by using MRI, EEG, and microbiome. The search was performed according to the requirements of a systematic review. In order to identify reports, we evaluated them following the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) criteria. Evidence synthesis: MRI and EEG have provided the advances to find features for PD over the last decade. Those techniques identify motor symptoms on substantia nigra where the patient shows a dopamine deficiency. However, over recent years, researchers have found that PD has prodromal phases, that is, PD is not simply a neurodegenerative disorder characterized by the dysfunction of dopaminergic. Thus, high field MRI, event-related potential (ERP) and microbiota data shows a significant change on the brain cortex, white and grey matter, the extrapyramidal system, brain signals and the gut.Conclusion: The structural MRI is a useful technique in detecting the stages of motor symptoms on the substantia nigra in patients with PD. The use of magnetic resonance as an early detector requires a high magnetic field, as to identify the areas which diagnose that the patient could be in the premotor stages. On the other hand, EEG performed well in detecting PD features. Furthermore, microbiome sequencing might include the classification of bacterial families that could help to detect PD in its prodromal phase. Thus, the combination of all these techniques can support the possibility of diagnosing PD in its very early stages.