The 1999 Australia Day Honours are appointments to various orders and honours to recognise and reward good works by Australian citizens. The list was announced on 26 January 1999 by the Governor General of Australia, Sir William Deane.

The Australia Day Honours are the first of the two major annual honours lists, the first announced to coincide with Australia Day (26 January), with the other being the Queen's Birthday Honours, which are announced on the second Monday in June.

Order of Australia Companion (AC) General Division Recipient Citation NotesProfessor Suzanne Cory For service to science as a leader in the field of biomedical research, to the advancement of the understanding of the molecular basis of cancer, and to the community as an advocate for improved science education in schools and universities Kaarene Noelle Fitzgerald For service to the community through commitment and support for Australian medical research into Sudden Infant Death Syndrome (SIDS), etc.Dr Malcolm Kenneth McIntosh For service to excellence in scientific and technological research, to providing new opportunities for industries, and to Australian Defence industry and science policyDr Lowitja (Lois) O'Donoghue, For public service through leadership to Indigenous and non-indigenous Australiansin the areas of human rights and social justice, particularly as chairperson of the Aboriginal and Torres Strait Islander Commission Nicholas Theodore James Paspaley For service to business development and trade, to the Australian pearling industry, and to the community

Officer (AO) General Division Recipient Citation NotesNorman Ross Adler For service to business and commerce, to the promotion of the arts in South Australia, and to the communityPaul Hunter Barratt For service to public administration, public policy development, business and international trade The Honourable Dr Jack Gordon Beale For service to the development of public policy in the areas of conservation, resource development and environmental engineering, and as a member of the New South Wales Parliament Brian Bull, For service to crime prevention through the promotion and implementation of the concept of community policing, to the Western Australia Police Service, and to the communityProfessor David James Burke For service to science and medicine, particularly in the field of clinical neurophysiology in the areas of research and education, and to the community through medical charities and lay organisations Alison Christine Bush For service to nursing and to the community, particularly in the provision of primary and maternal health care to Indigenous Australians and as an advocate of Indigenous Health Worker TrainingProfessor Donald John Chisholm For service to medicine and medical research as a leader in the fields of diabetes research, patient care, medical education and the organisation of medical services Dorothy Joan Dunn For service to the community, particularly as an advocate of the role of rural women in agricultural industry policy and as Foundation President of Australian Women in Agriculture Neil James Eagle For service to water resource management, to the citrus industry, and to the community, particularly through support for improved health services and aged care facilitiesTrevor James Flugge For service to the Australian grains industries in the areas of industry reform, research and development, and international grains marketingRosemary Irene Foot For service to the community, particularly in the areas of health, the visual arts, women's interests and politicsJoan Maie Freeman For service to science in the field of nuclear physics and to the environment as an advocate for social responsibility in scientific researchDr John Eugene (Fred) Gilligan For service to medicine, particularly intensive care medicine, and to the development of medical retrieval systemsJohn Edward Hatton For service to the community by raising public awareness of social issues and as an advocate for social change Thomas Andrew Hazell For service to multiculturalism, to the arts, to the Catholic Church in Melbourne, and to the community as a whole Sydney Howard For service in contributing to the success of community events and public celebrations as a leading international designer and operator of pyrotechnic displays, and to the community through support for charitable organisationsDr Graeme Thomas Killer For service to the veterans' community through commitment to enhancing health care services, and in the area of developing cost effective and improved health care for Defence personnelDr Alban Jude Lynch, For service to the mining industry, particularly in the area of research and education on the application of engineering technology in minerals processingHis Excellency John Philip McCarthy For service to the enhancement of Australia's international reputation and to the development of Australian regional policyGregory John Norman, For service to the community, particularly youth, through philanthropic support for research into treatments for childhood cancer and in the development of mentoring programmes for junior golfers Geraldine Marie Paton For service to the community through the media, medical research and the artsThe Honourable Peter Elliot Rae For service to business and commerce, to the Federal and Tasmanian Parliaments, and to the Aboriginal community of Flinders Island Margaret Critchley Smith For service to women in rural and remote areas as National President of the Country Women's Association of AustraliaRichard Harold (Dick) Smith For service to the community, particularly as a benefactor to charitable organisations, to business and commerce, and to the aviation industryDr Bruce William Stillman For service to scientific research in the field of molecular biology, particularly through the analysis of DNA replication in the living cellProfessor Geoffrey Ian Taylor For service to medicine in the field of plastic and reconstructive surgery, and the transfer of living bone grafts by utilising micro-vascular techniquesLeo Gerard Williams For service to Rugby Union football, to the law, and to the community

Military Division Branch Recipient Citation Notes Army Major General Peter James Dunn, For distinguished service to the Australian Army and the Australian Defence Force in the field of land force development, as the Military Head of the Defence Efficiency Review Secretariat and as the Head of the Defence Personnel Executive Personnel Air Force Air Vice-Marshal Peter Gervase Nicholson, For distinguished service to the Royal Australian Air Force, particularly as the Air Commander Australia

Member (AM) General Division