His most significant work is generally considered to be the trilogy The History of Bestiality, consisting of the novels Moment of Freedom (Frihetens Øyeblikk, 1966), Powderhouse (Kruttårnet, 1969) and The Silence (Stillheten, 1973).
Bjørneboe also wrote a number of plays, among them The Bird Lovers (Fugleelskerne, 1966), Semmelweis (1968) and Amputation (Amputasjon, 1970), a collaboration with Eugenio Barba and the Danish theatre ensemble Odin Teatret.