There is an increasing number of viral and bacterial pathogens suspected of contributing to asthma pathogenesis in childhood, making it more difficult for the practitioner to make specific therapy decisions. This review discusses the role of viruses, e.g. respiratory syncytial virus, human metapneumovirus, influenza viruses and rhinoviruses, as well as the role of the atypical bacteria Chlamydophila pneumoniae and Mycoplasma pneumoniae, as contributors to childhood asthma. Diagnosis, prevention, and therapy are discussed, including a summary of drugs, i.e. macrolide antibacterials, antivirals, and vaccine regimens already available, or at least in clinical trials. For the practitioner dealing with patients every day, drug regimens are assigned to the individual pathogens and an algorithm for the management of atypical infections in patients with asthma or recurrent wheezing is presented.