我國智慧財產法院已於2008年7月1日正式成立並開始運作，專責審理智慧財產權案件，並透過將刑事、民事、行政訴訟合而為一的審理制度，解決昔日智慧財產案件冗長審理的弊病，具有維持同一見解、加速審判速度、以及增進效率等功效。在智慧財產法院開始運作及審理法實施即將屆滿一年之際，本論文彙整智慧財產法院近一年來所審結之專利相關案件的判決來回顧審理法實施前專家學者之學理見解以及審理法實施後智慧財產法院實務見解兩者間之差異性，並且針對審理法的幾項重要特色從立法沿革、學者專家見解、法院實務見解等層面進一步加以討論。 本碩士論文共分為九個章節，除第一章緒論及第九章討論與建議外，其他章節主要針對新型態的智慧財產案件爭訟處理制度加以討論，相關主題包括智慧財產法院的成立背景、過程及其定位（第二章）、智慧財產案件審理法的特色，例如管轄權之劃分、設置技術審查官協助法官之案件審理、秘密保持命令制度、民、刑事訴訟關於權利有效性抗辯處理程序、專責機關參加訴訟、加強審理效率化、定暫時狀態處分程序、行政訴訟中容許提出新證據以及遠距視訊審理（第三章）；並針對具有相當爭議性之制度規劃進行討論，例如：專屬管轄與非專屬管轄（第四章）、專利權有效性之抗辯（第五章）、技術審查官與專責機關之參加專利訴訟（第六章）、專利行政訴訟中容許新證據之提出（第七章）、以及定暫時狀態處分之變革（第八章）。

民事訴訟法新修正後，新增了確定事、物現狀類型之證據保全，使當事人得利用法院調查蒐集之事證資料，以了解事實或物體之現狀。而為配合智慧財產案件其事證極易隱匿之性質，智慧財產案件審理法第18條第4項規定賦予證據保全制度直接強制力之效果，使證據保全成為智慧財產案件訴訟中具有直接強制力之蒐證手段。惟於智慧財產案件中，尤其是專利侵權案件，兩造多具有商業上之強烈競爭關係，且產品之競爭週期短暫，有可能產生一方當事人以證據保全之名義，實則卻係欲窺探對方商業或技術上營業秘密之行為，因此對於智慧財產證據保全案件之秘密保護即有其必要。而因美國和日本法制均設有秘密保持命令之制度，且為緩和秘密保護與訴訟審理主義間之衝突，故智慧財產案件審理法乃參照日本法之制度，引進秘密保持命令制度。依照目前我國智慧財產案件審理法第11至第15條之規定，秘密保持命令制度可能有以下若干值得討論之問題：秘密保持命令於證據保全程序之應用、法院對於秘密保持命令之審理於裁判、受秘密保持命令拘束之主體範圍以及違反秘密保持命令之刑事責任等，本論文即擬基於前開問題對於秘密保持命令制度進行介紹和提出未來展望。

我國於97年7月1日設立智慧財產法院，專責辦理智慧財產案件，智慧財產民事保全程序之假扣押、假處分及定暫時狀態處分亦包括在內，為瞭解智慧財產法院對於假扣押、假處分及定暫時狀態處分案件所採取之見解，本文蒐集智慧財產法院自97年7月1日設立後至103年4月30日止之假扣押、假處分及定暫時狀態處分裁定，將相關裁定之准許理由、駁回理由加以歸納分類，進行系統化之整理，依不同類型之權利如專利權、商標權、著作權等分類，予以統計分析，並提出問題與建議。

智慧財產案件審理法第16條揭示當事人抗辯智慧財產權有應撤銷、廢止之原因者，法院應就其主張或抗辯有無理由自為判斷，不適用相關法律停止訴訟程序之規定。前項情形，法院認有撤銷之原因時，智慧財產權人於該民事訴訟中不得對於他造主張權利。上開規定之意旨在於使同一智慧財產權所生之紛爭得於同一訴訟程序中一次解決，以對智慧財產權作有效保護。 依據上開規定，專利有效性之議題即可能為專利侵權訴訟程序及舉發程序所審理。兩程序審理之情形下，專利有效性之認定即可能會因對同一證據事實有不同見解而使認定結果產生歧異（嚴格定義下之判決歧異）或因證據/請求權基礎之不同而產生歧異（假性之判決歧異）。 民事法院和行政機關/法院於發明、新型及新式樣專利對專利有效性具兩歧認定之比例分別為所有抗辯專利有效性案件之6.8%、16%及12%。具歧異認定之案件中約有8%係因對同一證據之處理方式不同。約66%之案件係起因於呈送之證據有別及主張之撤銷理由不同，而此歧異認定或可於後續程序化解。另約有8%歧異認定之案件係因智慧局之見解受到先前經濟部對該見解之拘束，此分歧認定之結果或需藉由救濟程序才得化解。又約有16%具歧異認定之案件係因民事法院非以舉發程序中構成「舉發成立」之要件審酌系爭專利是否具撤銷事由，此歧異認定之結果尚需仰賴救濟程序始得化解。 民事法院倘非以舉發成立要件審酌專利有效性，則其審酌範疇可能涵蓋：得據以舉發事由、未達得據以舉發標準之事由、專利法及施行細則中得據以使申請案不予專利或不受理之事由。而有違誠信原則之事由亦可能受到審查，使系爭專利有不可執行之虞。倘民事訴訟有效性抗辯得涵蓋上開事由，則可預見本質不良但被智慧局誤准之專利將有去除之途徑，公眾利益即得以維護；專利申請人於申請過程中較可能考慮遵循誠信原則；且專利糾紛得以完全於一訴訟程序一併解決。專利環境或可能朝優質化、誠信化及效率化發展。於此架構下，侵權訴訟專利有效性抗辯機制及舉發程序之雙軌制審理即各有實質存在意義。 專利權人於台灣侵權訴訟具專利有效性抗辯案件之勝訴比約10%；敗訴案件中，發明、新型及新式樣專利被認定具無效事由之比例約為48%、65%及40%。審理法施行以來，舉發申請案之案件量約僅減少6%至7%，或隱含專利侵權訴訟不僅未於一定程度取代舉發制度更可能因而使當事人必需同時面對侵權訴訟與舉發程序雙軌戰場之處境。 審理法第16條之施行加快民事訴訟審結速度，達到迅速實現訴訟當事人權利保護之立法目的。而專利權所生之紛爭於同一訴訟程序中一次解決之目的，依檢驗角度之不同而有截然不同之結果，因此或可說未全然達到紛爭一次解決之立法目的。 / Article 16 of Intellectual Property Case Adjunction Act in Taiwan reveals that when a party claims or defends that an intellectual property right shall be cancelled, the court shall decide based on the merit of the case and the relevant laws concerning the stay of an action shall not apply.　Under the circumstances in the preceding paragraph, the holder of the intellectual property right shall not claim any rights during the civil action against the opposing party where the court has recognized the grounds for cancellation of the intellectual property right. The main purpose of the article is to solve the disputes over Intellectual Property Right in one litigation proceeding so as to protect the intellectual property right effectively. According to said article, the validity issue of a patent may be dealt with under civil litigation and invalidation proceedings. Under the circumstances, the decisions on the validity issue of a patent may be diverged due to different perceptions on the same evidence/fact (defined in this article as “actual decision divergence”) or different submitted evidences or instituted grounds (defined in this article as “fake decision divergence”). With respect to invention, utility model, and design patents, about 6.8%, 16% and 12% of cases with invalidity defense respectively had decision divergence between civil court and administrative organization/court. Among patents with decision divergence, around 8% of the patents were due to different perceptions of the same evidence. About 66% of the patents were deemed differently due to different evidences and instituted grounds. This discrepancy may be resolved in subsequent proceedings. Around 8% of the patents having divergent decisions were resulted from that the opinion of Taiwan Intellectual Property Office (TIPO) is confined by that in a previous administrative action issued by its superior organization, the Board of Appeal. This discrepancy may need to be resolved through a remedial procedure. Approximately 16% of the patents were determined differently because the civil court adopted different standards for initiating an invalidation action. This type of discrepancy may only be resolved through a remedial procedure. When the civil court uses its own standards in determining the validity issue of the patent in question, the scope of judicial review might include: the grounds of invalidation proceedings, the grounds of invalidation proceedings with loosened standards, the grounds attributed to a patent being rejected or an application to be inacceptable to TIPO based on Patent Act or the Enforcement Rules of Patent Act. In addition, inequitable conduct might also be reviewed. Under the circumstances, defective patents have a chance to be removed, a duty of candor and good faith would be more likely to be followed during prosecution; patent disputes are able to be reviewed entirely in one proceeding. It is expected that the quality of the patent system would be improved. Moreover, either the invalidity defense mechanism in infringement litigation, or the invalidation proceeding serves its own purpose. For patent infringement cases with invalidity defense, plaintiffs won about 10% of the cases. Among the cases lost by plaintiffs, the patent at issue deemed by civil court as invalid accounted for about 48%, 65% and 40% for invention, utility model and design patents respectively. Since the IP Case Adjudication Act took effect, the number of invalidation cases has decreased about 6-7%, which might indicate that the invalidity defense mechanism in infringement litigation does not replace the invalidation proceeding. The regulation of Article 16 of IP Case Adjudication Act speeds up civil proceedings indicating that the legislative purpose of providing effective protection to parties in IP litigation may be realized. However, the legislative purpose of solving patent disputes in one proceeding may not be achieved fully as the test results vary on the basis of different evaluation criteria.