The winged helix/forkhead transcription factors are characterized by a 100-amino-acid DNA-binding domain. The structure of the DNA-binding domain of hepatocyte nuclear factor 3γ (HNF3γ) has been solved. This domain folds into a variant of the helix-turn-helix motif and consists of three α-helices and two characteristic large loops, or "wings." Therefore, the DNA-binding motif is called the winged helix DNA-binding domain. Since the identification of the first member of this class, over 100 members have been identified in species ranging from yeast to human. The rapid accumulation of sequences has led to multiple names and classification systems, making it difficult to follow the literature. To address this, a proposal was developed to standardize the nomenclature for these proteins. Fox (Forkhead box) was adopted as the unified symbol for all chordate winged helix/forkhead transcription factors. A nomenclature committee was elected to implement this proposal. All Fox proteins contain the characteristic 100-amino-acid winged helix domain. Other portions of the Fox proteins are highly divergent. Phylogenetic analysis was used to delineate 15 subclasses for all known chordate Fox proteins. The analysis included sequences from GenBank and those submitted directly to the nomenclature committee. A neighbor-joining tree was generated using PAUP* 4.0. This phylogenetic tree will be updated regularly and may be downloaded from http://www.biology.pomona.edu/fox.html. Fox proteins are assigned to individual subclasses based on phylogenetic analysis. Subclasses are designated by a letter, and within each subclass, proteins are given an Arabic numeral. The actual name of any Fox protein is "Fox, subclass N, member X." Abbreviations for chordate Fox proteins follow specific capitalization rules. A new Fox protein is defined as a fully sequenced gene, cDNA, or protein that belongs to the Fox family based on sequence homology of its winged helix DNA-binding domain. A Fox Nomenclature website was established for submitting protein sequences. Investigators are encouraged to submit new sequences for assignment of the proper Fox name. These sequences will be kept confidential until publication. The unified nomenclature system was endorsed by over 20 scientists and the Human and Mouse Gene Nomenclature Committees. This system aims to standardize the naming of winged helix/forkhead transcription factors.The winged helix/forkhead transcription factors are characterized by a 100-amino-acid DNA-binding domain. The structure of the DNA-binding domain of hepatocyte nuclear factor 3γ (HNF3γ) has been solved. This domain folds into a variant of the helix-turn-helix motif and consists of three α-helices and two characteristic large loops, or "wings." Therefore, the DNA-binding motif is called the winged helix DNA-binding domain. Since the identification of the first member of this class, over 100 members have been identified in species ranging from yeast to human. The rapid accumulation of sequences has led to multiple names and classification systems, making it difficult to follow the literature. To address this, a proposal was developed to standardize the nomenclature for these proteins. Fox (Forkhead box) was adopted as the unified symbol for all chordate winged helix/forkhead transcription factors. A nomenclature committee was elected to implement this proposal. All Fox proteins contain the characteristic 100-amino-acid winged helix domain. Other portions of the Fox proteins are highly divergent. Phylogenetic analysis was used to delineate 15 subclasses for all known chordate Fox proteins. The analysis included sequences from GenBank and those submitted directly to the nomenclature committee. A neighbor-joining tree was generated using PAUP* 4.0. This phylogenetic tree will be updated regularly and may be downloaded from http://www.biology.pomona.edu/fox.html. Fox proteins are assigned to individual subclasses based on phylogenetic analysis. Subclasses are designated by a letter, and within each subclass, proteins are given an Arabic numeral. The actual name of any Fox protein is "Fox, subclass N, member X." Abbreviations for chordate Fox proteins follow specific capitalization rules. A new Fox protein is defined as a fully sequenced gene, cDNA, or protein that belongs to the Fox family based on sequence homology of its winged helix DNA-binding domain. A Fox Nomenclature website was established for submitting protein sequences. Investigators are encouraged to submit new sequences for assignment of the proper Fox name. These sequences will be kept confidential until publication. The unified nomenclature system was endorsed by over 20 scientists and the Human and Mouse Gene Nomenclature Committees. This system aims to standardize the naming of winged helix/forkhead transcription factors.