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Depreciation of rental properties are on Form 4562 (www.irs.gov/pub/irs-pdf/f4562.pdf) place in service during the first year in service. You should amended you tax returns for the first two years you filed Sch. E. for the rental properties. You will use MACRS and nonresidential real property recovery period of 27.5 years. Once you find the amount to deprecate your rental properties you will use that amount for 27.5 years or until you sell the properties.