Kazys Varnelis was born in Alsedziai, in 1917. He graduated from Kaunas Institute of Applied and Decorative Arts, where he studied decorative arts under the guidance of famous Lithuanian painter modernist Stasys Usinskas. From his early days he grew interested in history and collection. Having been encouraged by Head of the State Museum Paulius Galaune, the artist started collecting folk pieces of art while still being a student. The painter acquired the experience of a museologist while running the Museum of Ecclesiastical Art in Kaunas in 1941-1943. Kazys Varnelis spent two years studying at Vienna Fine Arts Academy (Akademie der Bildenden Künste) where he was granted a diploma (Akademischer Maler) in 1945. In 1949, he moved to the USA and settled in Chicago. In 1968, Varnelis was invited to give lectures at the Chicago City College, and was granted the title of a Professor in 1973.

This period played an extremely important role in the life of the painter. At that time, Varnelis developed his original painting style, which united the elements of constructivism, minimalism, and optic art. He gained a foothold in the Chicago modern art avant-garde, and organised personal exhibitions at the Museum of Contemporary Art in Chicago (in 1970), the Milwaukee Art Centre (in 1974), the University of Iowa Museum of Art (in 1975), and the Art Exhibition Palace in Vilnius (in 1988). The artist also took part in group exhibitions at the Art Institute of Chicago (Chicago and Vicinity Artists Show, in 1967, 1969, 1971, and 1974), the Washington Gallery of Art (The Corcoran, in 1973), the exhibition of abstractionists The Five in Chicago (in 1976), the exhibitions of Lithuanian painters Three Agendas organised at the National Mucsarnok Art Gallery in Budapest (in 1995) and the Tampere Art Museum in Finland (in 1996), the exhibition Group 24 at the Riga Contemporary Art Museum (in 1997), and many more. Various museums such as the Guggenheim Museum in New York, the Museum of Contemporary Art in Chicago, the Lithuanian Art Museum, the Art Institutes of Chicago and Akron, and private collectors have acquired various works produced by Kazys Varnelis.

The home of Gabriele and Kazys Varneliai in Chicago resembled a museum. In 1978, the family moved into a homestead Villa Virginia in Stockbridge (Massachusetts), in the spacious rooms of which they founded a constantly supplemented collection and library.

In 1998, following the restoration of the independence of Lithuania, painter and collector Varnelis together with his wife returned from the USA to Lithuania. With the help and support of the Ministry of Culture as well as Vilnius Academy of Arts, the Kazys Varnelis House-Museum was established in Vilnius. In 2003, the Kazys Varnelis House-Museum became a branch of the National Museum of Lithuania. In 1993, Kazys Varnelis was granted the honorary doctorate title by the Vilnius Academy of Arts.