BALTIMORE (AP) _ Milton S. Eisenhower, brother and confidant of President Dwight D. Eisenhower, troubleshooter for seven other presidents and head of three universities, has died at 85 after enjoying a long, busy retirement.

Eisenhower was in and out of Johns Hopkins Hospital for several months recently and, after five days' hospitalization, he died Thursday. University spokeswoman Sue Hartt said death was caused by numerous ailments.

Eisenhower spent his final years keeping up with baseball's Baltimore Orioles and working at his office at Johns Hopkins University, where he had rebuilt campus facilities and solidified the university's finances during an 11-year tenure as president.

Sen. Charles McC. Mathias said Eisenhower was ''generous in giving all his talent for the good of his country.'' Eisenhower's ''disciplined method of attacking problems has made a profound impression on me,'' the Maryland Republican said.

Eisenhower's health had been a problem since a bout with scarlet fever at age 4, and his eyesight grew so bad that in recent years he confined his recreational reading to large-type books mailed from the Library of Congress.

Milton Stover Eisenhower was born Sept. 15, 1899, in Abilene, Kan., the youngest son of David and Ida Stover Eisenhower. His six brothers were all good athletes, but he thought himself butter-fingered and decided to make himself a scholar and public servant. His brothers called him ''the smart one.''

He spent two years as city editor of The Abilene Daily Reflector before returning to Kansas State College to graduate in 1924. He briefly worked as an assistant professor of journalism before starting his long career in public service with a post in the Agriculture Department in 1926.

In 1927, he married and later had two children, Milton Stover Jr. and Ruth Eakin.

During World War II, he directed the relocation of Japanese-Americans from the West Coast, a policy he later regretted as an ''inhuman mistake,'' and the resettlement of refugees in North Africa after the Allied invasion in 1942. He also worked as a troubleshooter at several federal agencies

Early in the war, when Gen. Dwight Eisenhower was at the White House for a conference, President Franklin Roosevelt said, ''You know what I've been doing all morning? Well, I've been trying to decide among four competing bureaus where to put that baby brother of yours. He must be quite a man.''

Milton Eisenhower left the federal government in 1943 to become president of Kansas State University. He was named president of Penn State University in 1950 and served twice as president of Johns Hopkins, from 1956 to 1967 and again in 1971-72.

In his spare time, he helped President Harry Truman reorganize the Agriculture Department and negotiated for President John Kennedy with Fidel Castro in a failed effort to swap 500 tractors for 1,214 prisoners taken in the Bay of Pigs invasion.

Dwight Eisenhower often bounced his personal thoughts on important decisions off his brother, and assigned him to a fact-finding tour of Latin America.

The brother's admiration was mutual; Dwight Eisenhower thought his brother qualified to be president, while Milton wrote, ''I always thought he (Dwight) had the most logical mind I ever encountered.''

When Sen. Robert F. Kennedy and the Rev. Martin Luther King Jr. were assassinated in 1968, Johnson named him head of the Commission on Causes and Prevention of Violence. The report went to President Richard Nixon, but Eisenhower said he believed Nixon ignored the findings.

He published a book in 1974, ''The President is Calling,'' in which he assessed the eight presidents he advised, from Coolidge through Nixon.

He continued public pronouncements on national affairs, criticizing both President Reagan and former President Jimmy Carter for allowing the federal deficit to expand into what he termed a disaster.

Eisenhower is survived by his son, who lives in Scarsdale, N.Y., and four grandchildren.

A funeral was set for Saturday. Ms. Hartt said burial would be at a plot adjoining Eisenhower's wife, Helen, near the Penn State campus in State College, Pa.