A novel family of short interspersed nuclear elements (SINEs) has been identified in Fusarium oxysporum. This family has been called Foxy. The feature that makes Foxy unique among SINEs is the presence of 5' terminal tetranucleotide repeats. Both the number and the sequence of these repeats vary between individual members of the family. The genome of F. oxysporum f. sp. lycopersici contains at least 160 copies of Foxy. In a mutant obtained upon gamma irradiation of a wild-type isolate, 13 new Foxy insertions were identified. These observations, together with the occurrence of many Foxy-specific polymorphisms between isolates within one vegetative incompatibility group and the presence of Foxy-specific transcripts in the fungus, indicate that Foxy is currently active and may contribute to the genetic variability of F. oxysporum. Since we have not been able to detect Foxy sequences by PCR analyses in other fungi, this novel family of SINEs seems to be confined to Fusarium species.