Neonatal mortality in puppies is a problem frequently encountered by dog breeders. Often, only postmortem examination allows diagnosis and implementation of measures to save the rest of the litter. This article presents the key steps of the postmortem examination, namely, autopsy, histopathology, bacteriology, molecular identification of pathogens, and coproscopy. Sampling, samples' conservation, and interpretation of the obtained results are presented as well as their relative importance for the final diagnosis. Finally, examples of the most frequent syndromes observed under postmortem examination in canine newborns, together with the results from a complementary analysis looking for infectious agents responsible for death, are discussed.