A sensitive hemi-nested polymerase chain reaction (PCR) was used for detection of Melissococcus plutonius, the causative agent of European foulbrood (EFB). Sampling was made in Switzerland, where EFB is a widespread disease and incidences have increased in recent years. Larvae from brood samples with and without clinical signs of disease (n = 92) and honey (n = 92) from the same colonies were investigated. Individual larvae (n = 60) and pupae (n = 30) from diseased brood in single colonies were also investigated to study the distribution of the bacterium within the brood between larvae. M. plutonius was detected in larvae in all apiaries where symptoms of EFB could be seen, but not in all colonies judged as cases of EFB in the field, when healthy-looking larvae from such colonies were tested. The occurrence of the bacterium within the brood was not limited to larvae with symptoms only, but was mainly found in diseased larvae. The bacterium was also found in pupae. Healthy-looking larvae—even from heavily diseased combs—failed, in a number of cases, to amplify product in the PCR. M. plutonius could only be detected in 35% of the brood nest honey from clinically diseased colonies.