He was born the youngest of seven children to immigrant parents, both Slovaks, in Cleveland, Ohio, where he attended Cathedral Latin High School. At Marquette University he received his B.A. in 1960. He then entered the U.S. Navy as a communications officer, serving from 1961 to 1964. In 1967 he completed an M.A. at Columbia University.
Wilkes started his career as a writer for the Daily Camera in Boulder, Colorado from 1964 to 1966. He joined the Baltimore Sun from 1967 to 1968, then worked as a book editor for Harper & Row in New York City in 1969. The next year he joined Harper's Magazine Press as a book editor.
Wilkes has written for many magazines, including The New Yorker, New York Times Magazine, Atlantic Monthly, America, and Commonweal. In 1994 he published And They Shall be My People: An American Rabbi and His Congregation, the story of Congregation Beth Israel of Worcester, Massachusetts.
He is married to Tracy Gochberg. They have two children.
- Fitzgo: The Wild Dog of Central Park, nonfiction (Philadelphia: Lippincott, 1973)
- These Priests Stay, biography (New York: Simon & Schuster, 1973)
- You Don't Have to Be Rich to Own a Brownstone, nonfiction (New York: Quadrangle, 1973)
- Trying Out the Dream: A Year in the Life of an American Family, nonfiction (Philadelphia: Lippincott, 1975)
- Six American Families, biography (New York: United Church of Christ, 1977)
- Merton: By Those Who Knew Him Best, biography (San Francisco: Harper, 1984)
- In Mysterious Ways: The Death and Life of a Parish Priest, biography (New York: Random House, 1990)
- Companions along the Way, essays (Chicago: Thomas More Press, 1990)
- My Book of Bedtime Prayers, children's (Minneapolis: Augsburg, 1992)
- The Education of an Archbishop: Travels with Rembert Weakland, biography (Maryknoll: Orbis, 1992)
- Temptations, novel (New York: Random House, 1993)
- And They Shall Be My People: An American Rabbi and His Congregation, nonfiction (New York: Atlantic Monthly, 1994)
- The Good Enough Catholic: A Guide for the Perplexed, nonfiction (New York: Ballantine, 1996)
- The Seven Secrets of Successful Catholics, nonfiction (New York: Paulist Press, 1998)
- Beyond the Walls: Monastic Wisdom for Everyday Life, nonfiction (New York: Doubleday, 1999)
- Excellent Catholic Parishes: The Guide to the Best Places and Practices, nonfiction (New York: Paulist Press, 2001)
- Excellent Protestant Congregations: The Guide to the Best Places and Practices, nonfiction (Louisville: Westminster John Knox Press, 2001)
- Best Practices from America's Best Churches, editor, nonfiction (New York: Paulist Press, 2003)
- In Due Season: A Catholic Life, memoir (San Francisco: Jossey-Bass, 2009)
- Six American Families, documentary, Public Broadcasting Service (PBS), 1977
- Men of Iron, drama, Public Broadcasting Service (PBS), 1978
- The Molders of Troy, co-writer, drama, Public Broadcasting Service (PBS), 1980
- Merton, documentary, Public Broadcasting Service (PBS), 1984
- Source: Contemporary Authors Online. The Gale Group, 2004. PEN (Permanent Entry Number): 0000106241.