Her organically abstract paintings of one or two colors (the Infinity Nets series), which she began upon arriving in New York, garnered comparisons to the work of Jackson Pollock, Mark Rothko, and Barnett Newman. When she left New York she was practically forgotten as an artist until the late 1980s and 1990s, when a number of retrospectives revived international interest.
Following the success of the Japanese pavilion at the Venice Biennale in 1993, a dazzling mirrored room filled with small pumpkin sculptures in which she resided in color-coordinated magician's attire, Kusama went on to produce a huge, yellow pumpkin sculpture covered with an optical pattern of black spots. The pumpkin came to represent for her a kind of alter-ego or self-portrait.[37] Kusama's later installation I'm Here, but Nothing (2000–2008) is a simply furnished room consisting of table and chairs, place settings and bottles, armchairs and rugs, however its walls are tattooed with hundreds of fluorescent polka dots glowing in the UV light. The result is an endless infinite space where the self and everything in the room is obliterated.
The multi-part floating work Guidepost to the New Space, a series of rounded "humps" in fire-engine red with white polka dots, was displayed in Pandanus Lake. Perhaps one of Kusama's most notorious works, various versions of Narcissus Garden have been presented worldwide venues including Le Consortium, Dijon, 2000; Kunstverein Braunschweig, 2003; as part of the Whitney Biennial in Central Park, New York in 2004; and at the Jardin de Tuileries in Paris, 2010.
In her ninth decade, Kusama has continued to work as an artist. She has harkened back to earlier work by returning to drawing and painting; her work remained innovative and multi-disciplinary, and a 2012 exhibition displayed multiple acrylic-on-canvas works. Also featured was an exploration of infinite space in her Infinity Mirror rooms. These typically involve a cube-shaped room lined in mirrors, with water on the floor and flickering lights; these features suggest a pattern of life and death.
In 2017, a 50-year retrospective of her work opened at the Hirshhorn Museum in Washington, DC. The exhibit featured six Infinity Mirror rooms, and was scheduled to travel to five museums in the US and Canada.
On 25 February 2017, Kusama's All the Eternal Love I Have for the Pumpkins exhibit, one of the six components to her Infinity Mirror rooms at the Hirshhorn Museum, was temporarily closed for three days following damage to one of the exhibit's glowing pumpkin sculptures. The room, which measures 13 square feet and was filled with over 60 pumpkin sculptures, was one of the museum's most popular attractions ever. Allison Peck, a spokeswoman for the Hirshhorn, said in an interview that the museum "has never had a show with that kind of visitor demand", with the room averaging over 8,000 visitors between its opening and the date of its temporary closing. While there were conflicting media reports about the cost of the damaged sculpture and how exactly it was broken, Allison Peck stated that "there is no intrinsic value to the individual piece. It is a manufactured component to a larger piece." The exhibit was reconfigured to make up for the missing sculpture, and a new one was to be produced for the exhibit by Kusama.
Also in 2017, the Yayoi Kusama Museum opened in Tokyo, featuring her works.