A number of potential pitfalls exist in the histological diagnosis of cutaneous infectious diseases. These include inadequate clinico-pathological correlation, uncommon or unanticipated host reactions to a particular pathogen, overlooking subtle pathology, and lack of identification of dual or multiple pathology in a given sample. Failure to identify a virulent opportunistic infective organism may have grave consequences, especially in immuno-compromised individuals. Careful clinico-pathological correlation, astute observation, a high index of suspicion, careful scrutiny of additional sections and the judicious application of relevant special stains enable one to navigate around these daily diagnostic challenges and pitfalls.