Wolverine has been around for a long while, and whether it's clones or secret children appearing out of the woodworks, he's technically been a father from time-to-time. However, one Marvel Comics story implied that Logan might be the actual father of the powerful Avenger, Scarlet Witch.
Ultimates 3 by Jeph Loeb, Joe Madureira, Christian Lichtner and Richard Starkings is one of the most critically panned stories in Marvel Comics history. The main plot points in the book involves a sex tape, incest, and murder. Scarlet Witch is killed in the series and as the Ultimates investigate her murder. In Ultimates 3 #3, Wolverine reveals that it's fully possible that the magical mutant could actually be his daughter.
In the issue, Wolverine reveals to the rest of the team that Scarlet Witch could have been his daughter. He recounts the story of how after the war, he found refuge in the Balkan Mountains while searching for Wundagore so that a witch could end his life. As Wolverine collapses in the snow, he's rescued by a beautiful woman named Magda - Scarlet Witch and Quicksilver's mother. The two immediately have sex. But, mid-coitus Magneto, who had claimed Magda's heart for himself, arrived and sent Wolverine packing.
When Wolverine meets Magneto years later, he asked to track and kill Quicksilver. After Scarlet Witch stops Wolverine from killing her brother, Logan oversees the two of them having an incestuous relationship. It's an incredibly gross moment that's somehow even worse when you consider the fact Wolverine might be Scarlet Witch's dad. A father watching his potential daughter and her brother (who also would be Wolverine's son) having intercourse is about as messed up of a plotline as Marvel's ever published.
It's never officially confirmed that Scarlett Witch and Quicksilver were Wolverine's kids. But, it's strongly implied that it's a possibility. His relationship with Magda could have very well led to Logan being the actual father of the powerful twins instead of Magneto. Although considering the fact he had a first-row seat to the two's incestuous relationship, I'm sure he's OK with not being their dad. Wolverine very well could be the father to the two Avengers, but in this story, he's understandably not super eager to get to the bottom of the truth.