By around the third season, if you look closely, it appears that she's missing a tooth in the upper right part of her mouth.

Here's a commercial (https://www.youtube.com/watch?v=8V0THDy8zww) that Alyssa did back in 1986, where she "accidentally" walks into the Seaver family's house from Growing Pains and meets up with Kirk Cameron:
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Her missing tooth is quite noticeable at the 0:10 mark when she says, "You're Mike from Growing Pains!"

I was wondering if it was just my imagination or she really did lose a tooth sometime during the production of Who's the Boss?

Was she undergoing orthodontic treatment?

It's fairly common to have teeth extracted during the straightening process.

I almost like to believe that in storyline terms, Sam lost her tooth from a fight. Remember that in the pilot episode, she was getting beat up a lot, which is big reason why she and Tony had to leave Brooklyn. And in the later got into another scrap in the "Tony for President" (https://poddtoppen.se/podcast/1528039547/ay-oh-oh-ay-the-whos-the-boss-podcast/tony-for-president) episode from the second season.

By around the third season, if you look closely, it appears that she's missing a tooth in the upper right part of her mouth.

Here's a commercial that Alyssa did back in 1986, where she "accidentally" walks into the Seaver family's house from Growing Pains and meets up with Kirk Cameron:
mKGe8fgJHQ0

Her missing tooth is quite notable at the at the 0:10 mark when she says "You're Mike from Growing Pains!"

I was wondering if it was just my imagination or she really did lose a tooth sometime during the production of Who's the Boss?

I love this promo! Stuff like this blew me away when I was growing up but I never saw this one! I remember her tooth (from the intro of WTB) very clearly, but never noticed when it was gone. In this promo, wow it's like totally gone, like she got clocked in the face for cheating at a poker game or something lol. Still the hottest girl my brothers (and boys at my school) ever saw, she could've literally walked on set with dentures and no one would've cared

Was she undergoing orthodontic treatment?

It's fairly common to have teeth extracted during the straightening process.

It appears that Alyssa actually did wear braces (https://www.instagram.com/p/CfQz4HSDhc_/) when she wasn't working.

I love this promo! Stuff like this blew me away when I was growing up but I never saw this one! I remember her tooth (from the intro of WTB) very clearly, but never noticed when it was gone. In this promo, wow it's like totally gone, like she got clocked in the face for cheating at a poker game or something lol. Still the hottest girl my brothers (and boys at my school) ever saw, she could've literally walked on set with dentures and no one would've cared

It was sort of the meeting of arguably the two biggest teen idols (https://www.pinterest.com/pin/718535315525713039/) on television of that era.

I just started watching the reruns on IFC this week, started on season 3. I just noticed her missing tooth. I watched this show when I was a kid, never noticed til now.

I just saw the movie " The Long Island Lolita/ the Amy Fisher movie" yesterday . Alyssa played Amy. She did a great job !;)

FWIW she is also missing the same tooth on the other side of her mouth (her left side). it doesn't show as often as the one on the right side of her mouth but there are several shots in various episodes where it is as prominently displayed as it is in the screenshot in this thread of the missing tooth on the right side

I remember Jodie Sweetin (Full House) saying that she'd have to wear a fake tooth every time she lost a baby tooth (for continuity). I am surprised they didn't make Alyssa do the same thing.

It appears that Alyssa actually did wear braces (https://www.instagram.com/p/CfQz4HSDhc_/) when she wasn't working.

I never completely realized until recently how much Alyssa's son Milo (https://www.instagram.com/p/C3woGx3Lw1u/) looks like her as a child (https://www.youtube.com/watch?v=SFLHE4O1DQs), especially when they smile.