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General form for registration of securities under the Securities Act of 1933

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Registration No. 333-

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM S-1

REGISTRATION STATEMENT

Under

The Securities Act of 1933

CAPNIA, INC.

(Name of registrant in its charter)

1235 Radio Road, Suite 110

Redwood City, CA 94065

(650) 213-8444

(Address, Including Zip Code, and Telephone Number, Including Area Code, of Registrants Principal Executive Offices)

Anish Bhatnagar

Chief Executive Officer

Capnia, Inc.

1235 Radio Road, Suite 110

Redwood City, CA 94065

(650) 213-8444

(Name, Address, Including Zip Code, and Telephone Number, Including Area Code, of Agent for Service)

Copies to:

Elton Satusky, Esq.

Eric Hsu, Esq.

Wilson Sonsini Goodrich & Rosati,

Professional Corporation

650 Page Mill Road

Palo Alto, CA 94304

(650) 493-9300

Approximate date of proposed sale to the public: From time to time after this Registration Statement becomes effective.

If any securities being registered on this Form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, other than securities offered only in connection with dividend or interest reinvestment plans, check the following box: x

If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ¨

If this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ¨

If this Form is a post-effective amendment filed pursuant to Rule 462(d) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a small reporting company. See definitions of large accelerated filer, accelerated filer, and smaller reporting company in Rule 12b-2 of the Exchange Act. (Check one):

CALCULATION OF REGISTRATION FEE

The registrant hereby amends this registration statement on such date or dates as may be necessary to delay its effective date until the registrant shall file a further amendment which specifically states that this registration statement shall thereafter become effective in accordance with Section 8(a) of the Securities Act of 1933 or until the registration statement shall become effective on such date as the Securities and Exchange Commission, acting pursuant to said Section 8(a), may determine.

The information in this preliminary prospectus is not complete and may be changed. These securities may not be sold until the registration statement filed with the Securities and Exchange Commission is effective. This preliminary prospectus is not an offer to sell nor does it seek an offer to buy these securities in any jurisdiction where the offer or sale is not permitted.

The information in this prospectus is not complete and may be changed. The selling stockholder may not sell these securities until the registration statement filed with the Securities and Exchange Commission is effective. This prospectus is not an offer to sell these securities, and the selling stockholder is not soliciting offers to buy these securities, in any state where the offer or sale of these securities is not permitted.

SUBJECT TO COMPLETION, DATED NOVEMBER 19, 2015

PRELIMINARY PROSPECTUS

CAPNIA, INC.

10,000 Shares of Series A Convertible Preferred Stock (and 5,405,405 Shares of Common Stock Underlying the Series A Convertible Preferred Stock) and 2,702,704 Series D Common Stock Purchase Warrants to purchase 2,702,704 Shares of Common Stock (and 2,702,704 Shares of Common Stock upon Exercise of the Warrants) and 108,108 Placement Agent Warrants to purchase 108,108 shares of Common Stock (and 108,108 shares of Common Stock upon Exercise of the Warrants)

This prospectus relates to the sale of up to 10,000 Shares of our Series A Convertible Preferred Stock, which is convertible into 5,405,405 shares of our Common Stock, the issuance of 2,702,704 Series D Common Stock Purchase Warrants exercisable for an aggregate of 2,702,704 shares of our Common Stock at an exercise price equal to $2.46, in each case held by Sabby Healthcare Master Fund Ltd and Sabby Volatility Warrant Fund Ltd, which are funds managed by Sabby Management, LLC, and which we collectively refer to as Sabby, and 108,108 Placement Agent Warrants exercisable for an aggregate of 108,108 shares of our Common Stock at an exercise price equal to $2.46 (each, a selling stockholder and collectively, the selling stockholders); provided, however, that under the terms of the Series A Convertible Preferred Stock and the Series D Common Stock Purchase Warrants, in no event shall shares of Common Stock be issued to Sabby upon conversion of the Series A Convertible Preferred Stock or exercise of the Series D Common Stock Purchase Warrants to the extent such issuances of shares of Common Stock would result in Sabby having ownership in excess of 4.99%. The prices at which the selling stockholders may sell the shares of Common Stock underlying the securities held by them will be determined by the prevailing market price for the shares or in negotiated transactions. We will not receive proceeds from the sale of the shares by the selling stockholders. However, we may receive proceeds of up to approximately $10,000,000 from the sale of our securities to Sabby, pursuant to a Securities Purchase Agreement entered into with Sabby on October 12, 2015, or the Sabby Purchase Agreement. $4.5 million worth of Series A Convertible Preferred Stock was sold to Sabby on October 15, 2015, and the balance will be sold to Sabby once the registration statement, of which this prospectus is a part, is declared effective.

For a more detailed description of the Series A Convertible Preferred Stock, the Series D Common Stock Purchase Warrants, and the Placement Agent Warrants, see the section entitled Description of Securities.

Sabby is, and each of the other selling stockholders may be, an underwriter within the meaning of the Securities Act of 1933, as amended.

We will pay the expenses of registering these shares, but all selling and other expenses incurred by the selling stockholders will be paid by the selling stockholder.

Our Common Stock trades on the NASDAQ Capital Market, or NASDAQ, under the ticker symbol CAPN. On November 18, 2015, the last reported sale price per share of our Common Stock was $1.78 per share.

You should read this prospectus and any prospectus supplement, together with additional information described under the heading Available Information, carefully before you invest in any of our Common Stock.

Investing in our Common Stock involves a high degree of risk. Before making any investment in our Common Stock, you should read and carefully consider the risks described in this prospectus under Risk Factors beginning on page 10 of this prospectus.

Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or passed upon the adequacy or accuracy of this prospectus. Any representation to the contrary is a criminal offense.

This prospectus is dated , 2015.

TABLE OF CONTENTS

You should rely only on the information contained in this prospectus or any prospectus supplement or amendment thereto. We have not authorized anyone to provide you with different information.

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PROSPECTUS SUMMARY

This summary highlights information contained elsewhere in this prospectus and does not contain all of the information that you should consider in making your investment decision. Before deciding to invest in our securities, you should read this entire prospectus carefully, including the sections of this prospectus entitled Risk Factors and Managements Discussion and Analysis of Financial Condition and Results of Operations and our financial statements and related notes contained elsewhere in this prospectus. Unless the context otherwise requires, references in this prospectus to the Company, Capnia, we, us, and our refer to Capnia, Inc.

Company Overview

We are a diversified healthcare company that develops and commercializes innovative diagnostics, devices and therapeutics addressing unmet medical needs. Our first product, CoSense ® , aids in the diagnosis of hemolysis, a condition in which red blood cells degrade rapidly. When present in neonates with jaundice, hemolysis is a dangerous condition which can lead to adverse neurological outcomes. CoSense has 510(k) clearance for sale in the United States, or U.S., with a specific Indication for Use related to hemolysis issued, and has received CE Mark certification for sale in the European Union, or E.U. CoSense is commercially available in the U.S. CoSense combines a portable detection device with a single-use disposable sampling set to measure carbon monoxide, or CO, in the portion of the exhaled breath that originates from the deepest portion of the lung, which is referred to as the end-tidal component of the breath.

On September 8, 2015, through our wholly owned subsidiary, NeoForce, Inc., or NFI, we acquired substantially all of the assets of NeoForce Group, Inc., or NeoForce. As a result of this acquisition, we also develop and market innovative pulmonary resuscitation solutions for the inpatient and ambulatory neonatal markets. NFIs primary product is the T-piece resuscitator and related consumable, which delivers consistent pre-set inspiratory pressure and positive end-expiratory pressures. Other products include temperature probes, scales, surgical tables and surfaces.

Our therapeutic technology involves the use of precisely metered nasal carbon dioxide, or CO 2 , for the potential treatment of various diseases. Several randomized placebo-controlled trials have shown its efficacy in the symptomatic treatment of allergic rhinitis, or AR, and we continue to evaluate our options to further develop this product. In addition, we have recently announced new initiatives for the development of this technology for the treatment of trigeminally mediated pain disorders, such as cluster headache and trigeminal neuralgia, or TN. We have also applied for orphan drug designation for TN in the U.S. We have been interacting with the FDA and will continue the orphan drug designation process for TN. We have filed an IND with the FDA and intend to start a pilot clinical trial in 2015.

We continue to focus our research and development efforts on additional diagnostic products based on our Sensalyze Technology Platform, a portfolio of proprietary methods and devices which enables CoSense and can be applied to detect a variety of analytes in exhaled breath. Our current development pipeline includes proposed diagnostic devices for asthma in children, assessment of blood carbon dioxide, or CO 2 concentration in neonates and malabsorption. We may also license elements of our Sensalyze Technology Platform to other companies that have complimentary development of commercial capabilities.

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CoSense

Approximately 143 million babies are born annually worldwide, with approximately 9.2 million of these born in the U.S. and E.U. Over 60% of neonates present with jaundice at some point in the first five days of life. We believe CoSense has the potential to become a part of routine pre-discharge screening, by aiding in the differential diagnosis of hemolysis in infants that present with, or are at risk of developing, jaundice. Red blood cell breakdown is a normal phenomenon, but in certain situations the breakdown is accelerated or is excessive and is referred to as hemolysis. The most common cause of hospital readmission during the neonatal phase is jaundice, and we expect that CoSense will help reduce such readmissions. Many causes of jaundice do not represent a significant health threat. However, when severe jaundice occurs in the presence of hemolysis, rapid diagnosis and treatment may be necessary for infants to avoid life-long neurological impairment or other disability. Also, unnecessary treatment increases hospital expenses, is stressful for both infant and parents and may increase morbidity. There is an unmet need, therefore, for more accurate diagnostics for hemolysis, particularly if they are non-invasive, rapid, and easy to use.

CoSense detects hemolysis by measuring CO in the end-tidal component of the breath, and the measurement performed with CoSense is referred to as end-tidal carbon monoxide, or ETCO. The American Academy of Pediatrics, or AAP, guidelines, published in the journal Pediatrics in 2004, recommend ETCO measurement be performed to assess the presence of hemolysis in neonates requiring phototherapy, neonates unresponsive to phototherapy or readmitted for phototherapy and neonates with bilirubin levels approaching transfusion levels. These guidelines also note that ETCO is the only test that provides a direct measurement of bilirubin production because CO is a direct chemical byproduct of hemolysis. Therefore, ETCO provides a direct indication of the rate of bilirubin production from hemolysis. Measurement of serum bilirubin, whether performed via a transcutaneous bilirubinometer or via a conventional needle-stick assay, is...


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