He made the Twins out of Spring training, and made his major league debut against the Detroit Tigers in the second game of the season. He went 3-2 with a 3.79 ERA, and earned four saves in 49 games his rookie season, but was shut down late in the season due to a circulatory problem in his right arm. His role soon diminished as he spent the next two seasons going back-and-forth to the disabled list and doing rehab stints in the minors. In and, Naulty went a combined 1-3 with a 5.53 ERA and one save at the major league level. He tore his right groin off his pelvis in his final game as a Twin on July 11, 1998. Following the season, he was traded to the New York Yankees for minor league prospect Allen Butler. He went 1-0 with a 4.38 ERA doing mostly mop up duty with the Yankees. Though he did not make a post-season appearance, he earned a World Series ring with the Yankees in. After just one season in New York City, Naulty was traded to the Los Angeles Dodgers for minor league first baseman Nick Leach. The Dodgers released him during Spring training. He soon caught on with the Kansas City Royals, however, after just 1.2 innings with the Omaha Golden Spikes, in which he gave up eight walks and nine earned runs, he was released. After a brief stint with the independent Atlantic League's Atlantic City Surf, Naulty retired to become a pastor.
contacted Naulty in January as part of his investigation of performance-enhancing drug use by Major League Baseball players. He is first mentioned on page 232 of the Mitchell Report, and is very candid with his admissions. He is one few former and current baseball players interviewed by investigators to admit to using steroids, beginning in as a minor leaguer and continuing through his major league career. He also admits to using human growth hormone for one year, 1998, to recover from the groin injury. Naulty attributed his willingness to openly discuss his drug use to the remorse he felt. He told investigators, "if I could give back a little bit of something good, then I would like to." Shortly after the Mitchell Report came out, Naulty wrote an article for the New York Daily News detailing his drug use. He said he had access to, but did not use, steroids as far back as high school. Shortly after being drafted, he realized that in order to compete, he needed to throw harder, and add muscle to his thin 6'6" frame. Thus, he began taking anabolic steroids and amphetamines, and soon went from 185 pounds to 240, and added ten miles per hour to his fastball. The 1998 groin injury he attributes to having added more muscle to the major tendon in his groin than it is equipped to handle. Therefore, shortly after his trade to the Yankees, he began taking HGH. The negative impact of his drug use hit him later in his career when he thought about the fact that he took a roster spot from another player who was competing naturally. He fell into alcoholism, and began having severe mood swings from all the testosterone in his body. He claims that the night the Yankees won the World Series, he went out partying with friends, and was contemplating suicide by the end of the night. Naulty details a hard upbringing in an article published by Tom Verducci in the June 4, 2012 issue of Sports Illustrated. His older sister's heroin and crack cocaine addiction is what led to the decision for him to live with his father. Shortly after moving to Huntington Beach with his father, his father took a job in Kuwait that left Dan in the care of a baseball coach most of the time, who soon began sexually abusing him. Shortly afterwards, a female teacher also began abusing Naulty.
