The first clues for a paleolithic settlement of the area of Willendorf came from the discovery of "diluvial" bones and stone tools in the Brunner Brickyard (later Grossensteiner, and Merkel Brickyard). In late November 1883, Ferdinand Brun reports the discovery of a cultural horizon, belonging to the "Mammoth period" to the Natural History Museum Vienna (this site is now known as Willendorf I). Josef Szombathy is the first archaeologist to visit the site on December 5th, 1883. Under his supervision Brun conducts small excavations throughout 1884, this is followed by a first publication (Szombathy, 1884). The continuing exploitation of loess by the brickyard destroys the site of Willendorf I, but in 1889 Brun reports the discovery of animal bones and lithic remains in the Ebner Brickyard (Willendorf II).
Only limited work took place in the next years, but several publications described various collections from the site. Probably the most interesting is a report by Woldrich (1893) about the faunal remains, that also described the Willendorf I - 1 human femoral shaft.
Excavations were renewed on occasion of the building of the new railway line between Krems and Grein, from 1908 onwards. The excavations were led by Josef Szombathy (at the time director of the Anthropology Department of the Natural History Museum Vienna), but the local supervision was in the hands of Josef Bayer and Hugo Obermaier. Five new sites were discovered in the village of WIllendorf, numbered Willendorf III-VII. No proper excavation was undertaken at any of these, the work concentrated on Willendorf II and I.
After just a few days of work at Willendorf II, on August 7th, 1908 a worker discovered a small statue, underneath Layer 9. The Venus of Willendorf, as she became known, is one of the most famous examples of palaeolithic art. The excavations continued with interruptions until the start of World War I, and a smaller campaign took place in 1926.
In 1955, Fritz Felgenhauer re-excavated parts of the site to clarify the stratigraphy, in preparation for his monograph of the site (Felgenhauer, 1955).
Paul Haesaerts and colleagues undertook two section cleaning campaigns, to collect 14C and sedimentological samples in 1981 and 1993.