In 2010, Simon & Schuster published his book The Emperor of All Maladies: A Biography of Cancer detailing the evolution of diagnosis and treatment of human cancers from ancient Egypt to the latest developments in chemotherapy and targeted therapy. On 18 April 2011, the book won the annual Pulitzer Prize for General Non-Fiction; the citation called it "an elegant inquiry, at once clinical and personal, into the long history of an insidious disease that, despite treatment breakthroughs, still bedevils medical science." It was listed in the "All-Time 100 Nonfiction Books" (the 100 most influential books of the last century) and the "Top 10 Nonfiction Books of 2010" by Time in 2011. It was also listed in "The 10 Best Books of 2010" by The New York Times and "Top 10 Books of 2010" by O, The Oprah Magazine. In 2011, it was nominated as a National Book Critics Circle Award finalist.
Mukherjee's 2016 book The Gene: An Intimate History provides a history of genetic research, but also delves into the personal genetic history of the author's family, including mental illness. The book discusses the power of genetics in determining people's health and attributes, but it also has a cautionary tone to not let genetic predispositions define fate, a mentality that led to the rise of eugenics in history and something he thinks lacks the nuance required to understand something as complex as human beings. Harriet Hall describes Cancer and The Gene as "the story of science itself". The Gene was shortlisted for the Royal Society Insight Investment Science Book Prize 2016, "the Nobel Prize of science writing". The book was also the recipient of the 2017 Phi Beta Kappa Society Book Award in Science.
In his book The Song of the Cell, published in 2022, Mukherjee describes the history and medical mystery from the discovery of cell. Narrated in metaphors, many of which he created, such as "gunslinging sheriff for antibody and "gumshoe detective" to T cell, he tells the development of cell biology and how it became vital to modern medicine, from genetic engineering to immunotherapies. Suzanne O'Sullivan, reviewing in The Guardian, explains the book as a tool for "the reader to imagine they are an astronaut investigating the cell as if it is an unknown spacecraft." 2b1af7f3a8