Exhibit 99.1

Announcement

BOSTON, Massachusetts, United States, and SYDNEY, Australia – 13 September 2016 AEST.

GI Dynamics Inc. (ASX:GID) (the Company), a medical device company that provides an innovative treatment for type 2 diabetes and obesity, announces that it has received email correspondence from the Australian Therapeutic Goods Administration (TGA) indicating that the inclusion of the EndoBarrier device on the Australian Register of Therapeutic Goods (ARTG) may be cancelled.

EndoBarrier is currently included on the ARTG, which enables EndoBarrier to be sold commercially in Australia subject to the requirements of the Therapeutic Goods Act 1989 (Cth). EndoBarrier has been included on the ARTG since 2011.

On 20 May 2016, the Company announced that it had been in ongoing communication with the TGA regarding compliance-related matters. The Company provided all information requested by the TGA to it on 9 June 2016. The Company has now received email correspondence advising that the Medical Device Branch of the TGA has recommended that EndoBarrier’s inclusion on the ARTG be cancelled. Notice of the TGA’s decision in respect of such recommendation is expected to be received by the Company later this week. Should EndoBarrier’s inclusion on the ARTG be suspended or cancelled by the TGA, the Company will not be permitted to supply the EndoBarrier device in Australia.

The Company is continuing to discuss this matter with the TGA and will update the market in due course.

About GI Dynamics

GI Dynamics, Inc. (ASX: GID) is the developer of EndoBarrier^®, the first endoscopically delivered device therapy approved for the treatment of type 2 diabetes and obesity. EndoBarrier is approved and commercially available in multiple countries outside the United States. EndoBarrier is not approved for sale in the United States and is limited by federal law to investigational use only in the United States.

Founded in 2003, GI Dynamics is headquartered in Lexington, Massachusetts. For more information, please visit www.gidynamics.com.

Forward-Looking Statements

This announcement contains forward-looking statements concerning: our development and commercialization plans; our potential revenues and revenue growth, costs, excess inventory, profitability and financial performance; our ability to obtain reimbursement for our products; our clinical trials, and associated regulatory submissions and approvals; the number and location of commercial centers offering the EndoBarrier; and our intellectual property position. These forward-looking statements are based on the current estimates and expectations of future events by the management of GI Dynamics, Inc. as of the date of this announcement and are subject to a number of risks and uncertainties that could cause actual results to differ materially and adversely from those indicated in or implied by such forward- looking statements. These risks and uncertainties include, but are not limited to: risks associated with the consequences of terminating the ENDO Trial and the possibility that future clinical trials will not be successful or confirm earlier results; risks associated with obtaining funding from third parties; risks relating to the timing and costs of clinical trials, the timing of regulatory submissions, the timing, receipt and

www.gidynamics.com

GI Dynamics, Inc., is a corporation incorporated in Delaware, USA, whose stockholders have limited liability. ARBN 151 239 388

maintenance of regulatory approvals, the timing and amount of other expenses, and the timing and extent of third-party reimbursement; risks associated with commercial product sales, including product performance; competition; risks related to market acceptance of products; intellectual property risks; risks related to excess inventory; risks related to assumptions regarding the size of the available market, benefits of our products, product pricing, timing of product launches, future financial results and other factors including those described in our filings with the U.S. Securities and Exchange Commission. Given these uncertainties, you should not place undue reliance on these forward-looking statements. We do not assume any obligation to publicly update or revise any forward-looking statements, whether as a result of new information, future events or otherwise, unless required by law.

www.gidynamics.com

GI Dynamics, Inc., is a corporation incorporated in Delaware, USA, whose stockholders have limited liability. ARBN 151 239 388