Thomas Messer, whose leadership of the Solomon R. Guggenheim Museum over more than a quarter-century established its place among the world’s great museums of modern art, died Wednesday at his home in Manhattan. He was 93.

His death was confirmed by a family spokesman, Adam Lehner.

Messer became director of the museum in 1961, just two years after it moved into its famous building on Fifth Avenue with a spiral-ramp gallery, designed by Frank Lloyd Wright. He retired in 1988, as the Guggenheim Foundation, of which he had been director since 1980, was celebrating 50 years of supporting modern art.

During his tenure — one of the longest of a director of any major U.S. art museum — the Guggenheim deepened its collection, expanded its exhibitions program, vastly improved its publications and took its first step toward becoming a global institution.

Perhaps Messer’s most significant contributions were the acquisition of two magnificent private collections. In 1963, Justin Thannhauser, the son of a German art dealer, presented a significant portion of his collection, dozens of impressionist, post-impressionist and early modern works — including more than 30 by Picasso — to the Guggenheim as a permanent loan. That act immediately gave breadth to the museum’s collection, whose core has always had a 20th-century focus. (When Thannhauser died in 1976, those paintings became part of the Guggenheim’s holdings.)

In 1969, after years of ardent encouragement from Messer, Peggy Guggenheim agreed to exhibit a selection of cubist, surrealist and abstract expressionist works from her private collection at the museum that bears her family name — evidently no mean feat of persuasion, as the independent-minded Guggenheim spent much of her adulthood estranged from her family and was known not to admire the museum building. (It looked like “a huge garage,” she wrote in her autobiography.)

The exhibition was a success, and Guggenheim, who died in 1979, finally donated the whole of her collection, along with the Palazzo Venier dei Leoni, her former home on the Grand Canal in Venice, to the Guggenheim Foundation, which now operates it as a museum known as the Peggy Guggenheim Collection.

The gift not only strengthened the foundation’s holdings substantially — it includes Picasso, Braque, Kandinsky, de Chirico, Ernst and Pollock — but it also gave the Guggenheim its first foothold internationally. The museum has since opened the Guggenheim Museum Bilbao and the Deutsche Guggenheim Berlin (a 15-year partnership with Deutsche Bank to present exhibitions that concluded this year), and is planning a Guggenheim Abu Dhabi.

“It was due to Tom’s charm, grace, diplomacy and — and this is a point that none of us should ever forget — his love of great art that Peggy gave her collection and palazzo to the Guggenheim and not to the Tate,” Peter Lawson-Johnston, who was the Guggenheim’s president during Messer’s directorship, said at a celebration of Messer’s 90th birthday in 2010. He added: “Here we are, three decades later, with Guggenheims in Bilbao, Berlin, Venice and soon to be Abu Dhabi. The foundation for all this was laid by Tom Messer, and I can tell you, he laid that foundation under budget.”

Thomas Maria Messer was born in Bratislava, in what was then Czechoslovakia and is now Slovakia, on Feb. 9, 1920. His father was an art historian and a professor of German; his mother came from a family of musicians.

Although he himself had an artistic bent, he was sent to study chemistry, first in Prague and then in the United States, at Thiel College in Pennsylvania, though his travels abroad began inauspiciously. He left home Sept. 2, 1939, for England, whence he would cross the Atlantic. The next day England declared itself at war with Germany, and within hours the Athenia, the ship on which Messer was traveling, was torpedoed and sunk. He was rescued and subsequently made it to the United States on a different ship.

He eventually left Thiel — and chemistry — to study modern languages at Boston University, graduating in 1942. Afterward he joined the Army, serving in Europe as an interrogator for military intelligence. After the war he remained in Europe and formally studied art for the first time at the Sorbonne.

When he returned to the United States, he became director of a small museum in Roswell, N.M., and earned a master’s degree in art history from Harvard. Before landing at the Guggenheim, he was director of the Institute of Contemporary Art in Boston.

Messer leaves no immediate survivors. His wife, the former Remedios Garcia, died in 2002.