Kinsey's work, often associated with the Sexual Revolution in America in the 1960s, has generated substantial controversy since its publication. Since that time both Kinsey's work and private life have been the subject of an enduring controversy over the study of human sexuality (sometimes called sexology) and the impact of Kinsey's work on sexual morality.

Kinsey's research polarized a segment of society. Many in the Christian Right community felt that their religious and socially conservative views were in conflict with Kinsey's methods and underlying principles. They saw his supporters as dissolute libertines and his work as a morally corrupting force. Even today his name can elicit partisan rancor.

Kinsey's most prominent detractor is currently Judith A. Reisman, head of RSVPAmerica. Reisman alleges that Kinsey and his staff sexually abused children to produce some of the data in the Kinsey Reports. Kinsey Institute director John Bancroft claims that the subject of child/adult sexual interaction was deliberately chosen by Kinsey's opponents to discredit him because of the emotions surrounding it: "In recent years, when there has been anxiety bordering on hysteria about child sexual abuse, often resulting in circumstances where the accused is regarded as guilty until proved innocent, what better way to discredit someone?" The Kinsey Institute maintains Kinsey never had any sexual interaction with children, nor did he employ others to do so, and that he always interviewed children in the presence of their parents.

The Family Research Council (FRC) is another notable detractor. The FRC is a religious organization which wields substantial political clout among conservatives in the United States. The FRC echoes Reisman's claims of child/adult sexual interaction in their video The Children of Table 34, but that issue is not their primary focus. The FRC is primarily concerned with Kinsey's work on sexual orientation and homosexuality. Kinsey proposed that people do not fall into the categories of exclusive heterosexuality or exclusive homosexuality, but that most are between these extremes in a continuum of sexual orientations with homo- and heterosexuality at the extremes and bisexuality at the midpoint. The FRC sees Kinsey's work as a force that seeks to legitimize homosexuality, a sexual orientation the organization strongly opposes.

As a direct result of Kinsey's and other's works, in the 1960s the American Psychological Association removed homosexuality from its list of mental illnesses, refusing to continue endorsing it as something "odd" or needing to be corrected.

Aside from criticism of the implications of his research, Kinsey has been reported as participating in unusual sexual practices. In James H. Jones's biography Alfred C. Kinsey: A Public/Private Life, Kinsey is described as a bisexual masochist. He is also reported to have encouraged group sex with his graduate students, wife and staff. It is also known that Kinsey filmed sexual acts in the attic of his home during his research. Biographer Jonathan Gathorne-Hardy explains that this was to ensure the secrecy of these films which would certainly have been scandalous had the public become aware of them.

Some have suggested that the films Kinsey made are fundamentally pornographic in nature. Jones stated that Kinsey's wife had sex with other men, but that the couple remained married for 35 years in a relationship that remained sexual until Kinsey became ill near the end of his life. None of these accounts of Kinsey's own sex life are supported by official statements from the Kinsey Institute. Although some of them have been confirmed by independent multiple sources (such as his being bisexual), other claims are in dispute by the Kinsey Institute and others.