Who are you using?
For these situations you gotta look at your own characters' arsenals. Most, if not all, have normals or specials that beat lows.
For example:
Kim - far sC, far sD, sCD
Clark - far sD, sCD
Kyo - sD, HCB+K
Beni - far sD
King - sCD
It was funny the other day when I was playing against a Chin player with Kim and he was loving lows. Kim's sC kept going over Chin's lows and smacking him on the head, in desperation he did HCF+K to go under the kick but the sC smacked Chin on the head again lol.
Sweep tends to work quite well as well, as mentioned above.