Lower respiratory tract infections rank among the leading causes of morbidity and mortality worldwide. In clinical practice, especially in the care of severely ill patients, discrimination between tracheobronchial colonisation with potentially pathogenic microorganisms and infection is a common diagnostic challenge. While prompt antibiotic treatment is needed in critically ill patients with pneumonia, an inadequate use of antibiotics is the major cause for the emergence of drug-resistant microorganisms. The first part of this review provided a detailed overview of the currently available methods for the diagnosis of pulmonary infectious diseases. In the present second part of the manuscript, we focus upon methods and criteria for the differentiation between lower respiratory tract bacterial colonisation and lower respiratory tract infections, highlighting important pathogens.