Symptoms, such as fatigue are subjective perceptions that trigger patients to perceive them, take symptom management actions and evaluate the effects of those actions. This chain of events is dependent on personal, environmental and health and illness factors, in which this individual is embedded. For many subjective symptoms we have no objective biomarkers, which would provide information whether severity and duration of perceptions are in accordance with underlying biological mechanisms. Fatigue in HIV/AIDS patients is among the most bothersome and frequent symptoms experienced with and without antiretroviral treatments. Fatigue is defined as a perception of physical and mental exhaustion that is persistent over an extended period of time and causal relationships are complex. Mitochondrial intoxication, anemia, testosterone deficiency, elevated cytokine levels and sleepcycle changes have been identified with the presence and severity of fatigue. In order to understand the impact of fatigue in HIV infected individuals and treatments effects related to the nuclear and mitochondrial genome changes, a mitochondrial oligonucleotide microarray (MITO array) was designed and validated. Excellent reliability and validity were established and the MITO array was used to investigate skeletal muscle, subcutaneous muscle and peripheral blood samples. Subjective fatigue data and samples were taken from healthy controls and HIV/AIDS patients treated with a nucleoside reverse transcriptase-based treatment or untreated HIV/AIDS patients according to a mild-moderate-severe fatigue score. Principal component analysis revealed clear differences between the different tissue types. Hierarchical clustering did not distinguish healthy and mildly fatigue HIV patients on or off antiretroviral treatment. More samples from severely fatigued HIV patients are needed to identify group differences and investigate the mitochondrial impact of the HIV virus infection alone and in combination with antiretroviral treatments.