Singer Jimmy Scott performing at the Birdland in New York City in 2003. He died June 12 at 88. (Larry Busacca/Wireimage)

Jimmy Scott, a singer whose eerie, high-pitched voice had a haunting effect on listeners and who had a star-crossed career marked by hard luck, sorrow and decades of neglect before his late-stage revival, died June 12 at his home in Las Vegas. He was 88.

The death was confirmed by his biographer, David Ritz. The cause was not immediately disclosed.

Mr. Scott began singing in the 1940s and had one minor hit on the rhythm-and-blues charts during his career, with “Everybody’s Somebody’s Fool” in 1950. Even then — and typical of the misfortune that followed throughout his life — his name was not on the record: Credit was given to his bandleader at the time, Lionel Hampton.

Yet, even with limited exposure, Mr. Scott exerted a powerful influence over generations of singers who came after him, from Nancy Wilson and Dinah Washington to Frankie Valli, Marvin Gaye and Madonna, who once said, “Jimmy Scott is the only singer who makes me cry.”

Mr. Scott disappeared from view in the 1960s, when the album long considered his masterpiece, “Falling in Love Is Wonderful,” was pulled from the shelves in a legal dispute between record labels. It wasn’t until the 1990s that his career revived, with a series of new recordings and performances that continued into his 80s.

In 2000, arts writer Joseph Hooper described Mr. Scott in the New York Times as “perhaps the most unjustly ignored American singer of the 20th century.”

Even though his music was an acquired taste and his records sold in small numbers, Mr. Scott became something of a cultural touchstone. Documentary films were made about his life, a biography was written, and critics praised his idiosyncratic singing and his resilience after a life of adversity.

Entertainers as diverse as Billie Holiday, Liza Minnelli and David Byrne have admired Mr. Scott. Rock-and-roll star Lou Reed invited him on tour, saying Mr. Scott had “the most extraordinary voice I’ve ever heard in my life.” Director David Lynch used him in the final episode of his early 1990s cult TV show “Twin Peaks.” His songs appeared on the soundtracks of “Glengarry Glen Ross,” “Philadelphia” and other movies.

“Why is he not a household word as widely known as the many celebrities who have come under his spell?” jazz critic Will Friedwald wrote in the liner notes to Mr. Scott’s 2000 album “Mood Indigo.” “Yet there’s a deeper question than even that, one which defies any attempt at a reasonable explanation, and it is, how does Jimmy Scott move us so deeply and profoundly?”

People hearing Mr. Scott for the first time were invariably startled by his striking and preternaturally high singing voice, which was the range of a high alto but with a masculine strength.

Because of a hereditary hormonal condition later identified as Kallmann syndrome, Mr. Scott never went through puberty, and his voice did not change when he reached adolescence. He was slight of build, had no facial hair and stood only 4 feet 11 inches tall until he inexplicably grew several inches in his mid-30s. For years, he was billed as “Little Jimmy Scott.”

He was married five times and had a number of girlfriends, but he projected an androgynous ambiguity that led to humiliating and painful encounters.

“In my adult life, people have looked at me as an oddity,” he told David Ritz for the biography “Faith in Time: The Life of Jimmy Scott” (2002). “I’ve been called a queer, a little girl, an old woman, a freak, and a fag. As a singer, I’ve been criticized for sounding feminine. They say I don’t belong in any category, male or female, pop or jazz. But early on, I saw my suffering as my salvation.”

Mr. Scott transformed his difficulties into a dramatic, original style of singing. Although he could not read musical notation, he had a deep understanding of lyrics and was strongest at heart-stirring ballads, such as “I’ll Be Around,” “Sometimes I Feel Like a Motherless Child” and “Why Was I Born?

He sang at very slow tempos, which allowed him to elongate vowels and accent certain words, bringing fresh emotional meaning to oft-heard standards. With his eyes closed in concentration, his arms and hands danced at his sides, as if giving shape to the music. His singing seemed to be the very expression of a broken heart.

Music producer and impresario Quincy Jones, in a 1988 interview with the Village Voice, recalled seeing Mr. Scott perform in the 1950s: “He’d just stand there with his shoulders hunched and his eyes closed and his head tilted to one side. He sang like a horn — he sang with the melodic concept of an instrument. It’s a very emotional, soul-penetrating style. He’d put me on my knees, give me goose bumps. Jimmy used to tear my heart out every night.”

James Victor Scott was born in Cleveland on July 17, 1925, one of 10 children. His father was a road worker, and his mother played piano in a church.

Mr. Scott was 13 when his mother died; she had been struck by a car while trying to save her daughter crossing a street. Months earlier, he had stopped growing and learned about his genetic disorder, which also affected one of his brothers and two uncles.

His father could not keep the family together, and the children were dispersed to orphanages and foster homes. Mr. Scott, who never completed high school, worked as a theater usher and became a valet to a vaudeville dance team.

In 1944, he joined the traveling revue of Estelle “Caledonia” Young, a dancer and contortionist, and began singing in tent shows and small theaters throughout the Midwest. He joined Hampton’s band as a singer in 1948 and recorded “Everybody’s Somebody’s Fool,” which reached No. 6 on the Billboard R&B chart in 1950.

He worked on and off with Hampton until 1953 and performed that year at the first inauguration of President Dwight D. Eisenhower. (Forty years later, he sang at an inaugural ball for President Bill Clinton.)

Mr. Scott made a few recordings with small labels in the 1950s, including several with a group led by pianist Billy Taylor.

“I was astounded by Jimmy’s musicianship,” Taylor told biographer Ritz. “It didn’t matter that he couldn’t read or write music. His instincts for . . . phrasing were phenomenal. He interpreted the lyrics like Olivier interpreting Shakespeare.”

During the 1950s, Mr. Scott often performed in clubs in New York and New Jersey, and he made several recordings for Savoy, a label that miscast him as a rhythm-and-blues singer.

In 1963, Mr. Scott released “Falling in Love Is Wonderful,” an album of lushly arranged ballads that captured him at the peak of his vocal ability. Believing he was no longer under contract to Savoy, he recorded it for Ray Charles’s Tangerine label. When the album began to get radio airplay, Savoy’s owner, Herman Lubinsky, threatened legal action, claiming that his label had Mr. Scott under a lifetime contract. Because of the dispute, Mr. Scott’s record was taken off the shelves and was not re­released for 40 years.

When Lubinsky quashed the release of another album in 1969, Mr. Scott returned to Cleveland and all but abandoned his singing. He took a series of menial jobs, from busboy to fry cook to hospital orderly to shipping clerk.

He battled a drinking problem that, he admitted, contributed to divorces from his first four wives, Ophelia Sharon, Channie Booker, Ruth Taylor and Earlene Rodgers. Survivors include his wife of 10 years, Jeanie McCarthy Scott.

Mr. Scott remained mostly forgotten until the late 1980s, when broadcasters and journalists rediscovered him, and he began to make the occasional nightclub appearance.

Over the years, Mr. Scott was friends with many top musicians. One of the few who stayed in touch with him was Doc Pomus, a polio-stricken blues singer and songwriter whose hits included “This Magic Moment” and “Save the Last Dance for Me.”

Pomus had requested that Mr. Scott sing George and Ira Gershwin’s “Someone to Watch Over Me” at his funeral. Pomus died in 1991, and the crowd at his service was mesmerized when Mr. Scott began to sing, but few knew who he was.

One of the people at the funeral was Seymour Stein, an executive with Sire Records.

“Whispers went from row to row, ‘Who is it?’ ‘Who’s singing?’ — when suddenly I realized it could only be Little Jimmy Scott,” Stein told Ritz. “My God, I thought to myself, no one in the world can sing this soulfully.”

Contract negotiations began the next day, and in 1992, Mr. Scott released his first new recording in decades. “All the Way” received universal acclaim, hit No. 4 on the Billboard jazz chart and received a Grammy nomination. To a new generation of listeners, Mr. Scott’s peculiarly haunting vocal style was a revelation.

Other albums followed, along with international bookings, but Mr. Scott never quite attained the level of success many thought he deserved. His way of singing was just too rarefied for widespread fame.

Mr. Scott spent his final years in Las Vegas and continued to perform, sometimes in a wheelchair, until his mid-80s. Even then, the unmistakable voice was still there, penetrating and clear, sorrowful, serene and filled with pain and grace, all at once.

“All I needed was the courage to be me,” he told his biographer. “That courage took a lifetime to develop.”