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In the beginning of October this year Amazon announced per-second billing for EC2 instances. This potentially could be a big cost reduction for me. However Amazon also says this billing is platform dependent:

Per-second billing is not currently applicable to instances running Microsoft Windows or Linux distributions that have a separate hourly charge. Marketplace AMIs that do not have a separate hourly charge are eligible for per-second billing.

Does this new type of billing apply also to custom AMIs based on Amazon Linux? How can I check what kind of billing I have?

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The separate, hourly charge is a license fee in addition to the actual charge for the VM.

Amazon Linux does not have such a charge, unless your AMI is based on a Marketplace AMI that has an hourly license fee and also happens to be descended from Amazon Linux.

If you built these images yourself from the official and free Amazon Linux AMIs, then they should be eligible for per-second billing.