In an October 2003 interview with Songfacts, Alexakis explained the inspiration behind "Father of Mine":
That song is one of the very very few songs that are autobiographical. To answer your question, my feelings for my father haven't necessarily changed, but my feelings about myself after writing that song have been much better. It was a kind of catharsis to put those feelings into words, it's a way for me to get things out of my system. The song "Wonderful" is very much like that too. I was a child of a broken marriage, and my daughter was the child of a broken marriage, and it was hard to watch it happen to her. That was me trying to make sense of it.
I don't know (if my dad ever heard the song). I'm assuming he did. I know the two girls he raised, his step-daughters heard it and were mad at me about it.[4]
Music video
The music video, directed by Paul Hunter,[citation needed] starts with a young boy (played by Steven Anthony Lawrence) and his father spending time together. The father and mother get in a fight and the father leaves. The boy and mother then move to a black neighborhood (the boy is the only white person there). It skips to when the boy is a couple of years older and living in the neighborhood. He watches Everclear perform on TV. It then skips to when the boy is a teenager and hits the winning run at a baseball game while Art sings in the background. The baseball breaks through a window into an area where a group of rockers are hanging out. The video then shows clips from the different time periods in the boy's life and shows Art with his wife and kids. The video ends with the youngest boy following his dad out to the car as his dad drives off. It then shows the apartment he moved to and zooms out to the band playing in a room that overlooks the apartment.
