The confrontation of the differential and etiological diagnosis of the infectious diseases of cancer patients, including hematopoietic stem cells transplant (HSCT) recipients, must correspond to an informed, timely decision that directly affects medical behavior that determines a better survival and quality of life for patients. The main goal of this work was to contribute to the management of these patients developing a useful tool for the clinician to make these decisions. For that, infections were grouped by compromised systems, differentiating the possible etiological agents in bacteria, viruses, fungi and parasites, highlighting the relevant diagnostic tests, mentioning the recommended techniques together with the optimal sample type for proper processing. In addition, under each group of techniques we added the item "level of requirement" to suggest what, in the opinion of the authors and the existing evidence, must be mandatory to have at local level or can be derivable to another laboratory.