9. Common Stock

At Market Issuance Programs

In September 2012, the Company filed a shelf registration statement on Form S-3 (the “2012 Form S-3”) pursuant to which it could sell up to a total of $75.0 million of its equity securities and, in October 2012, entered into an At Market Issuance Sales Agreement with MLV & Co LLC (“MLV”) to issue and sell up to $30.0 million of shares of Common Stock under the 2012 Form S-3 (the “2012 ATM”). Upon completion of the 2012 ATM, in April 2013, the Company entered into a new At Market Issuance Sales Agreement with MLV whereby it could issue and sell up to $45.0 million of shares of Common Stock under the 2012 Form S-3 (the “2013 ATM”).

In July 2013, the Company filed a shelf registration statement on Form S-3 (the “2013 Form S-3”), which was declared effective on August 19, 2013.The Company may sell up to a total of $200.0 million of its equity securities under the 2013 Form S-3. In connection with the 2013 Form S-3, the Company amended its 2013 ATM with MLV such that it may offer and sell additional shares of Common Stock having an aggregate offering price of up to $70.0 million from time to time under the 2013 Form S-3 (the “Amended 2013 ATM”). Pursuant to the terms of the ATM’s with MLV, the Company will pay directly to MLV fees of up to 3% of the gross proceeds of the ATM then in effect. In the nine months ended September 30, 2013, the Company sold 10,352,219 shares of Common Stock under the ATMs and received net proceeds of $88.0 million. Since September 30, 2013 and through October 2, 2013, the Company sold an additional 206,203 shares of Common Stock for net proceeds of $1.4 million under the Amended 2013 ATM.

Authorized Shares

On September 30, 2013, the Company held a Special Meeting of Stockholders. At the meeting the Company’s Stockholders’ approved an amended and restated certificate of incorporation, to increase the number of authorized shares of capital stock from 65,000,000 shares to 115,000,000 shares and to increase the number of authorized shares of Common Stock from 50,000,000 to 100,000,000.

Stockholders’ Equity

The following table summarizes stockholders’ equity activity for the nine months ended September 30, 2013 ($000’s):

Stock-based Compensation Plans

The Company has three equity compensation plans, the Coronado Biosciences, Inc. 2007 Stock Incentive Plan, the Coronado Biosciences, Inc. 2013 Stock Incentive Plan, (the “2013 Plan”) and the 2012 Employee Stock Purchase Plan (the “ESPP”). At the Company’s Annual Meeting of Stockholders held on June 19, 2013, the stockholders approved the 2013 Plan, authorizing the Company to grant up to 2,300,000 shares of Common Stock to eligible employees, directors and consultants in the form of stock options, stock appreciation rights, restricted stock awards, and restricted stock unit awards. The Board of Directors determines the amount, terms and exercisability provisions of grants under the 2013 Plan.

Compensation Expense. The following table summarizes the stock-based compensation expense from awards, including stock options and restricted Common Stock awards to employees and non-employees, compensation expense for the ESPP and warrants to non-employees for the nine months ended September 30, 2013 and 2012, and from the period June 28, 2006 (date of inception) to date.

The following table summarizes stock option activity since December 31, 2012:

Total weighted average intrinsic value for all computations as of September 30, 2013 is based on the closing price of the Company’s common stock on September 30, 2013 of $7.01 per share.

As of September 30, 2013 the Company had unrecognized stock-based compensation expense related to unvested stock options to employees and non-employees of $9.1 million, which is expected to be recognized over the remaining weighted-average vesting period of 1.5 years.

On May 31, 2013, the Company issued 21,505 shares of Common Stock under Company’s Employee Stock Purchase Plan (“ESPP”). Common Stock was issued at $3.88 per share, which represents 85% of the closing price of $4.56 of the Common Stock on December 3, 2012.

Warrants to Purchase Common Stock

For the nine months ended September 30, 2013, the Company issued 80,705 shares of Common Stock pursuant to the cashless exercise of 158,429 warrants at a weighted average exercise price of $5.02, and 340 shares of Common Stock for cash proceeds of $1,098.