Are you talking about blossom end rot?
If so you can treat this by spraying a cal-mag supplement on the plant. I use MagiCal by Techniflora... 10ml/gallon of water once a week. Works for peppers also..
Thanks Lycan, That looks like what I have going on . My plants are just loaded with tomatoes, I wonder if I am too late to do anything about it this season ? The good thing is that I have way too many tomatoes anyway, I have a bunch like LBrandt mentioned and cherry tomatoes , they are delicious and no rot.