Science fiction
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"Greater Foundation" series
The Robot series was originally separate from the Foundation series. The Galactic Empire novels were originally published as independent stories. Later in life, Asimov synthesized them into a single coherent 'history' that appeared in the extension of the Foundation series.
The Robot series:
The Caves of Steel (1954), ISBN 0553293400 (first Elijah Baley SF-crime novel)
The Naked Sun (1957), ISBN 0553293397 (second Elijah Baley SF-crime novel)
The Robots of Dawn (1983), ISBN 0553299492 (third Elijah Baley SF-crime novel)
Robots and Empire (1985) (sequel to the Elijah Baley trilogy)
The Positronic Man (1993) (with Robert Silverberg, a novel based on Asimov's earlier short story "The Bicentennial Man")
Galactic Empire series:
Pebble in the Sky (1950)
The Stars, Like Dust (1951)
The Currents of Space (1952)
Original Foundation trilogy:
Foundation (1951), ISBN 0553293354
Foundation and Empire (1952), ISBN 0553293370
Second Foundation (1953), ISBN 0553293362
Extended Foundation series:
Foundation's Edge (1982), ISBN 0553293389
Foundation and Earth (1986), ISBN 0553587579
Prelude to Foundation (1988), ISBN 0553278398
Forward the Foundation (1993), ISBN 0385247931 (hardcover), ISBN 0553404881 (paperback)
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Novels not part of a series
The End of Eternity (1955) (Some readers think there is an oblique connection.)
Fantastic Voyage (1966) (a novelization of the movie featuring a team of American scientists traveling within a human body)
The Gods Themselves (1972)
Fantastic Voyage II: Destination Brain (1987) (not a sequel to the first Fantastic Voyage, but an independent story)
Nemesis (1989)
Nightfall (1990) (with Robert Silverberg, a novel based on the earlier short story)
The Ugly Little Boy (1992) (with Robert Silverberg, a novel based on an earlier short story)
(While primarily independent, some of these novels have very minor connections to the Foundation series.)
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Short story collections
Also see List of short stories by Isaac Asimov
I, Robot (1950), ISBN 0553294385
The Martian Way and Other Stories (1955)
Earth Is Room Enough (1957)
Nine Tomorrows (1959)
The Rest of the Robots (1964)
Nightfall and Other Stories (1969)
The Early Asimov (1972)
The Best of Isaac Asimov (1973)
Buy Jupiter and Other Stories (1975)
The Bicentennial Man and Other Stories (1976)
The Complete Robot (1982)
The Winds of Change and Other Stories (1983)
The Alternate Asimovs (1986)
The Best Science Fiction of Isaac Asimov (1986)
Robot Dreams (1986)
Azazel (1988)
Gold (1990)
Robot Visions (1990) ISBN 0-451-45064-7
Magic (1995)
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Mysteries
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Novels
The Death Dealers (1958) (later republished as A Whiff of Death)
Murder at the ABA (1976) (also published as Authorized Murder)
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Short story collections
Black Widowers and others
Asimov's Mysteries (1968)
Tales of the Black Widowers (1974)
More Tales of the Black Widowers (1976)
The Key Word and Other Mysteries (1977)
Casebook of the Black Widowers (1980)
The Union Club Mysteries (1983)
Banquets of the Black Widowers (1984)
The Disappearing Man and Other Mysteries (1985)
The Best Mysteries of Isaac Asimov (1986)
Puzzles of the Black Widowers (1990)
Return of the Black Widowers (2003) contains stories uncollected at the time of Asimov's death, in addition to contributions by Charles Ardai and Harlan Ellison
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Nonfiction
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Popular science
Collections of columns from the Magazine of Fantasy and Science Fiction
Fact and Fancy (1962)
View from a Height (1963)
Adding a Dimension (1964)
Of Time, Space, & Other Things (1965)
From Earth to Heaven (1966)
Science, Numbers and I (1968)
The Solar System and Back (1970)
The Stars in Their Course (1971)
Left Hand of the Electron (1972)
The Tragedy of the Moon (1973)
Of Matters Great & Small (1975)
The Planet that Wasn't (1976)
Quasar, Quasar, Burning Bright (1977)
Road to Infinity (1979)
The Sun Shines Bright (1981)
Counting the Eons (1983)
X Stands for Unknown (1984)
The Subatomic Monster (1985)
Far as Human Eye Could See (1987)
The Relativity of Wrong (1988)
Out of Everywhere (1990)
The Secret of The Universe (1990)
Others
Asimov on Numbers (1959)
Asimov's Chronology of Science and Discovery (1989, second edition extends to 1993)
Asimov's Chronology of the World (1991)
The Chemicals of Life (1954)
The Clock We Live On (1959)
The Collapsing Universe (1977) ISBN 0-671-81738-8
The Earth (2004, revised by Richard Hantula)
Exploring the Earth and the Cosmos (1982)
The Human Brain (1964)
Inside the Atom (1956)
Isaac Asimov's Guide to Earth and Space (1991)
The Intelligent Man's Guide to Science (1965)
Jupiter (2004, revised by Richard Hantula)
Life and Energy (1962)
The Neutrino (1966)
Our World in Space (1974)
The Sun (2003, revised by Richard Hantula)
The Universe: From Flat Earth to Quasar (1966)
Venus (2004, revised by Richard Hantula)
Views of the Universe (1981)
Words of Science and the History Behind Them (1959)
The World of Carbon (1958)
The World of Nitrogen (1958)
Isaac Asimov's Treasury of Humor (1971)
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Annotations
Asimov's Annotated "Don Juan"
Asimov's Annotated "Paradise Lost"
Asimov's Annotated Gilbert and Sullivan
The Annotated "Gulliver's Travels"
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Guides
Asimov's Guide to the Bible, vols I and II (1981), ISBN 0-517-34582-X
Asimov's Guide to Shakespeare
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Other
Opus 100 (1969)
The Sensuous Dirty Old Man (1971)
Asimov's Biographical Encyclopedia of Science and Technology (1972)
Opus 200 (1979)
Isaac Asimov's Book of Facts (1979)
The Roving Mind (1983) (collection of essays). New edition published by Prometheus Books, 1997, ISBN 1-57392-181-5.