Baldwin was born April 3, 1958, in Amityville, New York, and raised in the Nassau Shores neighborhood of nearby Massapequa, the eldest son of Carol Newcomb (nee Martineau; born 1930) and Alexander Rae Baldwin Jr. (October 26, 1927 - April 15, 1983), a high school history/social studies teacher and football coach. He has three younger brothers, Daniel, William, and Stephen, who also became actors. He also has two sisters, Beth and Jane. Alec and his siblings were raised as Roman Catholics.

In 1990, Baldwin met actress Kim Basinger when they played lovers in the film The Marrying Man. They married in 1993 and had a daughter, Ireland, in 1995. They separated in 2000, and finalized a divorce in 2002.  Baldwin chronicled his seven-year battle to remain a part of his daughter's life in his 2008 book, co-authored with Mark Tabb, A Promise to Ourselves: A Journey Through Fatherhood and Divorce. Baldwin contends that after their separation in December 2000, his former wife, Kim Basinger, endeavored to deny him access to his daughter by refusing to discuss parenting, blocking visitation, not providing telephone access, not following court orders, not dropping their daughter off for reasons of convenience, and directly lobbying the child. He contends that she spent over $1.5 million in the effort. Baldwin called this parental alienation syndrome.  Baldwin has called the attorneys in the case "opportunists", and has characterized Basinger's psychologists as part of the "divorce industry". He has faulted them more than Basinger, and writes, "In fact, I blame my ex-wife least of all for what has transpired. She is a person, like many of us, doing the best she can with what she has. She is a litigant, and therefore, one who walks into a courtroom and is never offered anything other than what is served there. Nothing off the menu, ever." Baldwin wrote that he spent over a million dollars, has had to put time aside from his career, has had to travel extensively, and needed to find a house in California (he lived in New York), so that he could stay in his daughter's life.  Baldwin contended that after seven years of these issues, he hit a breaking point, and on April 11, 2007, left an angry voicemail message in response to another unanswered arranged call, in which Baldwin called his 11-year-old daughter a "rude, thoughtless little pig". He contends that the tape was sold to TMZ which released the recording, despite laws against publishing media related to a minor without the permission of both parents. Baldwin admitted that he made a mistake, but asked not to be judged as a parent based on a bad moment. He later admitted to Playboy in June 2009 that he contemplated suicide over the voicemail that leaked to the public. Of the incident, he said, "I spoke to a lot of professionals, who helped me. If I committed suicide, [ex-wife Kim Basinger's side] would have considered that a victory. Destroying me was their avowed goal."  In late 2008, Baldwin toured in support of the book, speaking about his experiences related in it.

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