Since the mid-1980s, observations of marine animals with alopecia have been reported worldwide, although in most cases specific causes and consequences have not been elucidated. Adding to that list, an unprecedented feather loss condition affecting ∼1 in 1000 adult Adelie penguins was observed at the beginning of December 2011 at each of three colonies on Ross Island, Antarctica. Feather loss was again observed in 2012-13 and 2013-14. The condition was characterised by irregular patches of bare skin on various parts of the body well before the usual period of moult. Blood samples, plucked feathers and cloacal swabs were obtained to investigate the cause or causes of this abnormal loss of feathers. No ectoparasites were detected on physical inspection of any birds or by scanning electron microscopy of feathers removed from birds experiencing feather loss. Blood smears were negative for hemoparasites. There was statistical support for mild lymphocytosis and moderate basophilia from the results of white blood-cell differentials in penguins with feather loss compared with those with no feather loss. Blood samples were negative to a PCR diagnostic specific for beak and feather disease virus. Three new putative RNA viruses were detected by high-throughput sequencing of cloacal samples, showing similarity to rotaviruses, astroviruses and picornaviruses. Although the significance of these viruses is not known, extended investigation into this feather loss condition is needed.