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Get them both down to 48.9% or below. That gets them both out of maxed territory, which beats one less card with a non-zero balance.
I agree with Heaven, if you are trying to improve you credit score. Alternatively, if you are trying to save money pay the one with the highest APR.
Fee
Pay the 99% utilization cards to under 48.9% and put anything leftover towards the highest APR balances.
I am carrying some 0% balances on two cards that caused each to have 65% ish utilization. I just paid them down to under 48.9% and my other two cards to $0 and I got a 20 point bump in my scores.
Even if you don't need the bump, I just feel like 99% screams danger and should be dealt with ASAP.
Do put yourself on a good budget and don't let those cards get ran up again.
@Anonymous wrote:
I am at 43% utilization. Owe $23146 out of $54500 available. I have 2 cards at 99% utilization, 1 card at 55%, and the rest are at 0. I am about to get a bonus of $12000. Should I pay the 2 cards down to 50%? Should I pay 1 completely off and a little on the other?
Pay 2 cards down to 49% and the third to as low as you can get it.
To our OP --
Remember that you are also paying interest on those cards. Therefore if you pay the cards to precisely 48.99%, then the next month's interest charge will put you back over that line. Thus, when you are paying interest, it's a good idea to aim for about 2% less than the benchmark you are hearing from the folks here. E.g. aim for 47%.
Another thought is to place some of that money in savings, so that you will be able to confidently pay more than the minimum payment each month on every card going forward. Paying only the minimum payment is a flag for risk in the eyes of a CC issuer. (Though the 99% utilization is a far more serious flag.)