The disease normally starts when fungi infect the flowers or young fruit. These latent infections lie dormant as the fruit develops. Once the fruit starts to ripen, the disease develops rapidly, leaving no sign of the disease on the outside of the fruit.

Internal rot in capsicums can be caused by five different organisms, which infect the fruit in different ways. There has been very little research on the control of this disease in Australia, although a number of detailed studies have been conducted internationally over the last 30 years.

Hortus Technical Services undertook a study of 18 capsicum fruit collected from 6 different growers in the Bundaberg region in July 2015. The study found internal fungal rots in 78% of the fruit, and concluded the predominant cause was latent infection by the fungus, Alternaria alternata.