Infections are one of the most common complications after hematopoietic stem cell transplantation (HSCT). Diagnosis is established by analysis of clinical symptoms and results of diagnostic tests such as biochemical panels, microbiological cultures, and visual diagnostics. As the microbiological cultures yield positive results in only some patients and visual diagnostics might miss the infectious source, the diagnosis and proper treatment often depends on clinical assessment supported by laboratory test results. The most commonly used makers of inflammation include C-reactive protein and procalcitonin. However, these tests have serious limitations when used in patients after HSCT. The drugs used in conditioning, neutropenia, and graft-versus-host disease might influence the results of the tests and misguide the physician. In this review, we summarize the current knowledge on profiles of expression of basic markers of inflammation used in clinical practice in patients after HSCT.