What is the difference between the smallest six digit whole number and the greatest four digit whole number

The smallest six digit number, assuming repetitions are allowed, is 100,000.
The largest four digit number, also assuming with repetitions, is 9,999.

To calculate the difference, subtract the smaller number from the larger number:

100,000 - 9,999
= 90,001

So the difference between the smallest 6 digit whole number and the largest 4 digit whole number is 90,001.