Microorganisms interact continuously with animal hosts. Occasionally this leads to infection and disease in the host. Detection and identification of an infecting microorganism depends on good sampling technique, competent laboratory methodology and an understanding of the pathogenicity of specific microorganisms. This chapter looks at collection and storage of samples for culture, microscopy and staining, bacterial and fungal identification, significance of bacterial isolates, PCR testing, antigen detection and serology, antimicrobial susceptibility testing, in-practice bacterial culture and antimicrobial susceptibility testing and multidrug-resistant bacterial pathogens. The chapter also includes case examples.