You can deduct property taxes included with the second mortgage if they are listed on the 1098 form as having been paid by the mortgage company for the second loan. If both forms show an amount for property taxes, then the deduction can be taken.
Form 1098 from different lenders may read slightly differently. Often if there is not a specific box showing Real Estate Taxes paid, it may be toward the bottom of the statement under the Escrow Reconciliation area as Taxes Paid. Some lenders report Real Estate Taxes paid on the back side of the statement.
Please see this TurboTax Help article with information to enter Form 1098.
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