I had a quick look at Google Finance (Financials, Annual Data) and I see the following for 2012: Amazon's total operating expenses as a percentage of revenue was 98.2%. Costco's was 97.2%. Wal-mart's was 94.1%. Based on this data, you might argue that Amazon has a cost disadvantage relative to both Costco and Wal-mart. But before reaching any conclusions you would need to back out Amazon Web Services and the Kindle (from Amazon) [1].
As a quick and dirty analysis, we can back out the $2.909b Amazon invested in R&D in 2012. Note, neither Costco nor Wal-mart have a line item for R&D. In this case, Amazon's operating expenses as a percentage of revenue is 92%, or about 5% less than Costco's and 2% less than Wal-mart's. [2]
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[1] You might also want to back out Sam's Club from Wal-mart.
[2] Given Amazon has revenues that are just 11% of Wal-mart's, you could argue that Amazon's cost advantage will likely increase as it further scales revenue and operations.
You made very good points w.r.t. Sam's Club for Walmart or Kindle for Amazon. One needs to adjust the data in order to be precise. The effect though is probably second order and shouldn't change the picture that much. At least it seems consistent with my own anecdotal experience.
It is also that possible Amazon's expense is exaggerated by accelerated depreciation. In the expansion phase if your facility is not fully utilized you get dinged again on appreciation. WalMart owns a lot of real estate and has capitalized lease as well I think so some of the operational cost may show up as interest expenses. To get a true picture one needs to account for all those as well.
The beauty of Amazon's model is that it uses little to no capital (all operations can be funded by negative working capital and other liabilities incidental to operations), so it can expand unconstrained by capital needs, as long as it can find new customers.