Wethey wrote a number of books, among them, Colonial Architecture and Sculpture in Peru, El Greco and His School in two volumes, Alonso Cano, a study of the 17th- century Spanish painter, and three volumes on Titian. Wethey had also contributed three articles in Encyclopædia Britannica: "El Greco", "Titian" and "History of Western Architecture".
The publishing of El Greco and His School in 1962 had a huge impact in scholarly circles. In 1937 a highly influential study by art historian Rodolfo Pallucchini had the effect of greatly increasing the number of works accepted to be by Spanish Renaissance painter El Greco. Palluchini attributed to El Greco a small triptych in the Galleria Estense at Modena on the basis of a signature on the painting on the back of the central panel on the Modena triptych. There was consensus that the triptych was indeed an early work of El Greco and, therefore, Pallucchini's publication became the yardstick for attributions to the artist. Nevertheless, Wethey denied that the Modena triptych had any connection at all with the artist and, in 1962, produced El Greco and His School, a reactive catalogue raisonné, with a greatly reduced corpus of materials. Whereas art historian José Camón Aznar had attributed between 787 and 829 paintings to the Cretan master, Wethey reduced the number to 285 authentic works and Halldor Sœhner, a German researcher of Spanish art, recognized only 137. Wethey and other scholars rejected the notion that Crete took any part in his formation and supported the elimination of a series of works from El Greco's oeuvre. Since 1962 the discovery of the Dormition of the Virgin and an extensive archival research initiated by other scholars, such as Nikolaos Panayotakis, Pandelis Prevelakis and Maria Constantoudaki, gradually convinced the academic world that Wethey's assessments were not entirely correct, and that his catalogue decisions may have distorted the perception of the whole nature of El Greco's origins, development and oeuvre. The discovery of the Dormition led to the attribution of three other signed works of "Doménicos" to El Greco and then to the acceptance of more works as authentic - some signed, some not, - which were brought into the group of early works of El Greco. Even Wethey accepted that "he probably had painted the little and much disputed triptych in the Galleria Estense at Modena before he left Crete". Nevertheless, disputes over the exact number of El Greco's authentic works remain unresolved, and the status of Wethey's catalogue raisonné is at the centre of these disagreements.