Sarfati was a founder of the Wellington Christian Apologetics Society in New Zealand, and has long retained an interest in Christian apologetics and the creation–evolution controversy. His first two books, Refuting Evolution in 1999, and Refuting Evolution 2 in 2002, are intended as rebuttals to the National Academy of Sciences publication Teaching about Evolution and the Nature of Science and the PBS/Nova series Evolution, respectively. Refuting Compromise, published in 2004, is Sarfatis rebuttal of the day-age creationist teachings of Hugh Ross, who attempts to harmonise the Genesis account of creation with mainstream science regarding the age of the Earth and the possible size of the Biblical Flood, against which Sarfati defends a literal biblical timeline and a global flood. Eugenie Scott and Glenn Branch of the National Center for Science Education called Sarfatis Refuting Evolution 2' a "crude piece of propaganda".
Sarfati is a critic of geocentrism, the Myth of the flat Earth and flat Earth teaching, homosexual behaviour, and abortion except to save the life of the mother.  While opposing embryonic stem cell research, he supports adult stem cell research. Sarfati also supports vaccination and rebuts anti-vaccination arguments.