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If there is a theft loss of inventory - generally there are two options. The first and may be the simplest is to deduct them is by adding the value to the cost of goods sold. For instance if you are a sole proprietor - that amount is reported on Schedule C
Schedule C, line 39 - http://www.irs.gov/pub/irs-pdf/f1040sc.pdf
Another way is to report them on IRS Form 4684, Casualties and Thefts. Section B is used for business or income-producing property. - http://www.irs.gov/pub/irs-pdf/f4684.pdf
For losses involving business-use property, refer to Publication 584B, Business Casualty, Disaster, and Theft Loss Workbook. - http://www.irs.gov/pub/irs-pdf/p584b.pdf