傷齒龍科的化石是第一群被敘述的恐龍化石之一。最初,在1856年約瑟夫·萊迪(Joseph Leidy)將這些動物分類於蜥蜴亞目;但在1924年,查爾斯·懷特尼·吉爾摩爾(Charles W. Gilmore)將牠們分類於恐龍總目的鳥臀目。直到1945年,查爾斯·斯騰伯格(Charles Mortram Sternberg)將傷齒龍科鑑定、分類於獸腳亞目。1969年以來,傷齒龍科與馳龍科共同屬於恐爪龍下目演化支。但在1994年,湯瑪斯·霍茲(Thomas R. Holtz Jr)根據加大的腦部、長而低的上頜孔等特徵,建立了Bullatosauria,包含了似鳥龍下目與傷齒龍科。傷齒龍科的骨盆也顯示牠們較馳龍科原始。在中國新發現的原始傷齒龍科化石,例如中國獵龍與寐龍,顯示出傷齒龍科、馳龍科、以及原始鳥類始祖鳥之間的相似處;而現在的大多數古生物學家,包括霍爾特在內,都認為傷齒龍科較接近鳥類,而離似鳥龍下目較遠,使得Bullatosauria分類遭到廢棄。
由Theropod Working Group成員所進行的密集獸腳亞目研究,顯示基礎馳龍科恐龍、傷齒龍科、以及始祖鳥之間有非常相似的地方。這幾個分類形成近鳥類演化支,該演化支由奧尼拉斯·諾瓦斯與迪亞戈·玻爾所提出[11]。Hwang等人所提出的演化樹,顯示始祖鳥代表近鳥類的一個原始分支,而馳龍科與傷齒龍科較為先進。這個理論提升了恐爪龍類演化出空氣動力行為的可能性[12]。
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