He has three daughters - Bubbles, Blossom and Buttercup, but they were artificially created using a secret formula containing sugar, spice and everything nice (like the nursery rhyme about what little girls are made of), but he accidentally added chemical X to the mixture, so the girls were born with super powers. Professor Utonium is inspired by retro 50's TV-type dads, and he tries to raise the Powerpuff Girls as normally as possible even though they have to go and fight monsters and criminals. The original 1990's cartoon was amazing but the 2016 version totally blows. In that cartoon Utonium had a fourth Powerpuff Girl named Bliss, but it was stupid and no one can see it as canon and call themselves a Powerpuffs fan.
Oh, and in the 90's cartoon the PPGs themselves once created a new girl named Bunny. But they didn't have all the right ingredients to make the formula, so Bunny was born hunchbacked and homely and kind of slow and dumb. When the girls instruct her on how to be a crimefighter, Bunny messes up at first and beats up all the police and sets the criminals free. She makes up for her mistakes, however, and makes the other girls happy and proud. But then suddenly she just started shaking and blew up. Apparently the formula used to create Bunny was too unstable, but it was really sad.