The emerging of the internet and world wide web as enabler of electronic commerce has resulted in some complexities for accountants in conducting their engagement. In electronic commerce, which trading activities have been facilitated with computer network such as intranet, extranet or internet, internal control structure has become more complicated than those without network. Confidentiality, integrity, authenticity and non-repudiation are some of the major complex issues in the application of electronic commerce these days.Those complexities, which do not occur in non computer-based trading, are based on the fact that electronic commerce not only involves accounting disiplines but also technical comprehension from other diciplines. Accountants find difficulties in facing the internal control issues in computer-based information system environment, especially in a situation that business has already been implementing computer network in conducting its primary and support activities. This article will discuss material related to the current issues of internal control structure, the implication of electronic commerce on internal control structure and opportunities for accountants.