Muscular fatigue may result from HIV infection, and may be associated with antiretroviral drug treatment. Clinical features linked to muscle biopsy findings may assist in determining etiology, and guide treatment decisions. This case series examined HIV patients in an ambulatory HIV clinic who received antiretroviral therapy, and complained of unexplained muscular fatigue. Clinical features with measurement of acid-base status, levels of lactate, aminotransferases, triglycerides and creatine kinase were correlated to light and electron microscopic results of muscle biopsy. Three patients with acquired mitochondrial changes on biopsy shared common features of lactatemia, elevated aminotransferases and triglycerides, and ultrasonographic hepatic steatosis. A fourth patient with normal mitochondria had myositis with fibrosis, but no systemic symptoms. Biochemical parameters were unremarkable, except for a high creatine kinase. Acquired mitochondrial disease may manifest as systemic illness and muscular fatigue. Unique metabolic changes and other organ dysfunction may precede overt physical signs of HIV myopathy.