Tax Audit Against PT A in few years have led law uncertainty for PT A’s goodwill amortization expense as a deductible expense on taxable income calculation. The uncertainty is reflected in tax assessment letter which inconsistence led correction on PT A’s goodwill amortization expense in tax year has been audited. The arguments are used by the DGT to make correction also look contradictive with the accounting standard and taxation regulation. Therefore, this study is aimed to analyze the arguments used by Directorate General of Taxation (DGT) in make tax treatment on PT A’s goodwill amortization expense which arise from acquisition seen from the accounting standard and taxation regulation. Moreover, this study also aimed to analyze the tax treatment on the PT A’s goodwill amortization expenses which applied by the Directorate General of Taxation seen from the principle of legal certainty. This study uses qualitative method and data collection technique which used by author is literature studies and field research by interviewing key informant. Based on findings and discussion, PT A’s goodwill arising from the acquisition of PT B PT D, and PT E should remain and exist on the financial statements, thereof goodwill amortization expenses are deductible expense on taxable income calculation. The principle of legal certainty in the tax treatment applied by DGT to PT A also have not been fully met. Thus, the result of this study is the argument used by the DGT regarding the tax treatment of PT A’s goodwill amortization expense is contradictive and do not comply with accounting standard and tax regulations. Moreover, the tax treatment on PT A’s goodwill amortization expense applied by DGT are not fully met the principle of legal certainty.