Smallpox was a variable yet often fatal viral infectious disease. Even with good nursing, it regularly killed around 30% of recognised cases. Though widespread in Europe and Asia, it was probably unknown in southern Australia when the first British colony began in 1788.

It never became widely established among the colonists, killing only about 100 of them over the next 100 years, and mostly in port-city outbreaks that were traced to visiting ships. Yet a smallpox outbreak in 1789 devastated the Aboriginal people near the Sydney colony, killing perhaps half of them, while sparing the British.

This imbalance leads some medical experts to argue that the main agent of death during major outbreaks of "smallpox" in 1789 and in 1829–1831 was in fact chickenpox. This is a disease to which the British were largely immune but which, in a virgin soil epidemic, can produce symptoms very similar to smallpox. Doctors began to distinguish smallpox more clearly from chickenpox in the early to mid-nineteenth century; and during the 1829–1831 outbreak there was vigorous debate among the colony’s surgeons as to which disease it was, with the chief surgeon favouring chickenpox.

However, most historians have called the 1789 and 1829–1831 diseases smallpox. Smallpox is commonly described as the main or one of the main diseases that reduced the Aboriginal peoples and left them unable to resist European settlement. Debate among modern medical and historical experts as to the identity of the deadly 1789 disease, how it reached Australia, and why it did not infect any of the British (though it killed two non-Europeans who were living inside the British colony) is ongoing.

Overview European colonisation of Australia was accompanied by epidemic diseases to which the original inhabitants had little resistance. Colds, influenzas, tuberculosis (TB), and measles were major killers. Such diseases devastated Aboriginal populations, weakened their cultures, and often left them in no position to resist the newcomers. Within perhaps as little as six months of the arrival of the First Fleet, venereal disease was already a serious problem for local Aboriginal peoples; but the first disease to produce a major fall in the Aboriginal population around Sydney was the 1789 outbreak, some 16 months after the Fleet arrived, of what Governor Phillip and others referred to as "smallpox". Watkin Tench, a captain in the Marines, wrote that,Tench, "A Complete Account of the Settlement at Port Jackson". quoted in "Towards more consistent estimates of Aboriginal de-population in the early colonial Australia" by John Carmody and Boyd Hunter, Asia-Pacific Economic & Business History conference, 2014, p. 12. (page refs. are to the online version).

A full list of smallpox outbreaks in Australia falls into two main groups. Firstly, there were three widely-spaced "Aboriginal" epidemics which devastated Aboriginal populations but largely spared the colonists.Cumpston (1914) p. 3. Two of these outbreaks were recorded in New South Wales: in 1789 and in 1830. Later there was a long-running outbreak in the 1860s, which spread through much of Northern and Western Australia and down to the Great Australian Bight in the south.Flood, Josephine (2019) "The Original Australians", Sydney, Allen and Unwin, pp. 30–35. In the second group, there were six major ship-borne outbreaks in the nineteenth century, in 1857, 1868–1869, 1871, 1881–1882, 1884–1886, 1887 and 1893.Note that Cumpston agrees that there were three separate fatal epidemics among the Aboriginals, but lists as many as eleven "in the settlements", as reckoned by a review in "Book Notices" on 22 May 1915. These were successfully confined to port cities, and predominantly affected European colonists. Thereafter, further brushes with imported smallpox were relatively minor.For details up to 1923 see The History of Smallpox in Australia 1909-1923 , by J. H. L. Cumpston and F. McCallum, Australian Commonwealth Department of Health, Service Publications no. 29, 1923.

Although the electron microscope, which is capable of seeing and distinguishing viruses, did not begin to become available to doctors until the 1940s, there is little doubt that at least the second group of outbreaks were true smallpox. They had its typical death-rate of around one death per four recorded infections, and its relatively slow infection rate.See Carmody and Hunter (2014), p. 10. They did not selectively kill Aboriginal persons, and there was no mystery as to their origin. In total this second group killed about one hundred people.

The first group of outbreaks, which primarily affected non-Europeans, was more deadly, spread more rapidly, and had a much greater effect upon the history of Australia and the current situation of its Aboriginal peoples. The historian Judy Campbell remarks,Invisible Invaders: Smallpox and Other Diseases in Aboriginal Australia 1780–1880, Melbourne University Press, 2002, p. 227.

The 1789 outbreak, in particular, has been much debated. Several medical experts and anthropologists have argued that it cannot have been smallpox and was probably chickenpox—a highly infectious disease, with partly similar symptoms, to which Europeans though not Aboriginals had considerable immunity. The famous virologist Frank Fenner, who played a major role in the worldwide elimination of smallpox, remarked in 1985:

Since Fenner's 1985 remarks, further historical evidence has been produced, and opinions have hardened. The medical experts Ford and Carmody insist that the failure of the 1789 outbreak to affect Europeans, despite what they consider abundant opportunities, rules out smallpox;Darkiñung Recognition An Analysis of the Historiography for the Aborigines from the Hawkesbury-Hunter Ranges to the Northwest of Sydney by G. E. Ford [PhD, ANU] 2010 MA thesis in history, University of Sydney 2010, pp. 34–35, cf. pp. 11, 32 yet most historians continue to prefer the traditional view that it was smallpox. The extent to which smallpox and chickenpox in 1789 were seen as separate diseases is a grey area.

Among those who believe the disease was smallpox, there are two main theories: that it was introduced from Sulawesi in Indonesia by Macassan traders, and that it was brought directly to south-eastern Australia by European ships. Some, like the independent scholar Christopher Warren, have insisted both that the disease was smallpox and that it was probably released by British colonists in a deliberate act of biological warfare. This view has resonated with some Aboriginal authorities, including professors Maynard and Langton, and the medical officer Dr Mark Wenitong.Marcia Langton on First Australians, Episode 1, TV program October 2008, (accessed 28 November 2021). However, the historians Henry Reynolds, Peter Dowling, and Cassandra Pybus still regard this theory as unproven.See section below: "Deliberate release theories, 1789".

Outbreaks Outbreak of 1789 This disease swiftly inflicted a huge toll on the local Eora population of Aboriginals, causing most of those not infected to flee the region. The epidemic probably began in March 1789, and "subsided by early May". Early in April 1789, British observers noticed the sudden disappearance of the "native canoes" from the Harbour's many coves, investigated, and described the pitiable conditions of the sick or dying Aboriginal persons they discovered there.

The naval officer William Bradley who sailed into Sydney on 9 May 1789 was shocked, noting that some of those abandoned in rock shelters seemed to have died of thirst while too sick to seek water, and that children had often perished beside a dead parent.William Bradley's Voyage to New South Wales edited by Colin Choat at Project Gutenberg Australia, State Library of New South Wales, 2019 (based on William Bradley's Journal, December 1786 — May 1792), p. 162. Busby, as mentioned below, made similar suggestions in 1831. Another naval officer John Hunter agreed that thirst or hunger had increased the mortality of sufferers "immediately deserted by their friends and left to perish in their helpless situation for want of sustenance".John Hunter, An Historical Journal of the Transactions at Port Jackson [...] 1787-1792, 1793, John Stockdale, London, p.143; Robert Barnes, An Unlikely Leader: The Life and Times of Captain John Hunter, Sydney University Press, 2009, pp. 151-152. Judy Campbell in her 2002 book Invisible Invaders summed up that the disease's initial impact in 1789 "was especially severe because of shock, flight, and fear, as well as the virus itself".Campbell p. 98. Bradley, unlike Tench, thought it an open question whether the Aboriginal peoples were previously "strangers" to smallpox,Bradley p. 162: "whether they were strangers to it before is doubtful". while Lieutenant King in his journal was sure they were not;Cumpston p. 166. and this has remained a point of contention among historians. Most point to the lack of visible scarring at first contact; but some, including Robert Barnes and Alan Frost, feel that since three observers, King, Hunter and Collins "demonstrated that the Aboriginals had a name for it", the disease was more likely a pre-existing, if infrequent, visitor.Barnes, 2009, pp. 164-165.

The precise proportion of Aboriginal peoples that perished is difficult to determine, though Governor Phillip estimated that perhaps half had died; and the Aboriginal Bennelong also believed that half the Eora in the Sydney district had died.Campbell, p. 101. After a few weeks the canoes returned, and 20 were seen passing Sydney Cove on 2 June 1789;Bradley p.164. but Phillip's expeditions in subsequent months showed him that the disease, if it began near Sydney, had rapidly moved on to nearby Aboriginal populations.Ford (2010), pp. 33 ff., 62 ff.

The Aboriginal peoples do not seem to have associated this disease with the settlement. In mid-1788, they had shown strong resentment of the colony, with several spearings; but by 1791 they had become regular peaceful visitors, even to the Governor's House, as depicted in William Bradley's watercolours.Bradley 2019 pp. 225; see also the on-line report Archaeological investigation Conservatorium site Macquarie Street, Sydney], vol 1, Casey and Lowe, 2002, pp. 6-9. John Hunter noted, "before I left Port Jackson, the natives very familiar and intimate with every person in the settlement; many of them took up their rest every night in some of the gentlemen's houses".Hunter 1793, p. 210; cf. Tench (1979) p.192. Yet, in 1789 the outbreak reduced not just the number of Aboriginal persons living near the new settlement but also their fighting strength and presumably their confidence in their culture. The historian Peter Dowling argues that it probably put an end to any possibility of Aboriginals attacking and destroying the colony in its first years.Compare Judy Campbell, Invisible Invaders, 2002, pp. 161, 189, 213.

Like smallpox, this outbreak produced abundant small pustules which often left permanent scarring on survivors. Though it is probable that other recently-introduced diseases were already at work,Carmody and Hunter (2014), p. 10. it is clear that this pustular disease was the main killer of Aboriginal persons. Carmody and Hunter calculated in 2014Carmody and Hunter (2014) p. 14. See also a summary by Ross Gittins in the Sydney Morning Herald. that if the disease was really smallpox it would have caused some 30 to 50 recorded cases within the colony, especially among the 84 children.Carmody and Hunter (2014), pp. 12-13. Those who believe the disease was smallpox counter-argue that in early 1789 there was simply not enough contact with the colonists for the disease to reach them.e.g. Fenner (1985)