Program disturb is reduced in a non-volatile storage system during a programming operation by determining a susceptibility of a set of storage elements to program disturb and taking a corresponding precautionary measure, if needed, to reduce the likelihood of program disturb occurring. During programming of a lower page of data, a natural threshold voltage distribution of the set of storage elements is determined by tracking storage elements which are programmed to a particular state, and determining how many program pulses are need for a number N1 and a number N2>N1 of the storage elements to reach the particular state. Temperature and word line position can also be used to determine the susceptibility to program disturb. A precautionary measure can involve using a higher pass voltage, or abandoning programming of an upper page of data or an entire block. In some cases, programming continues with no precautionary measure.