Infections caused by parasites and fungi can trigger the cytokine storm syndrome (CSS). These infections causing CSS can occur together with acquired immunodeficiencies, lymphomas, the use of immunosuppressive medications, transplant recipients, cancer, autoinflammatory, and autoimmune diseases or less frequently in healthy individuals. Histoplasma, Leishmania, Plasmodium, and Toxoplasma are the most frequent organisms associated with a CSS. It is very important to determine a previous travel history when evaluating a patient with a CSS triggered by these organisms as this may be the clue to the causal agent. Even though CSS is treated with specific therapies, an effort to find the causal organism should be carried out since the treatment of the infectious organism may stop the CSS. Diagnosing a CSS in the presence of parasitic or fungal sepsis should also lead to the study of an altered cytotoxic or hemophagocytic response in the susceptible host.