Historically, the State-by-State requirements that an out of State company doing business in the State file papers in order to qualify to do business in the State was deemed to be no more than an "excuse me" requirement … failure to file (paying State taxes is a different question) meant disqualification to file a complaint in State courts, a defect which could be fixed without penalty as the occasion arose. In a typical transactional document, the representations and warranties of the seller to investors or a buyer would say, in effect, that no State filings had been neglected if failure to file would have a material adverse effect.
Now, the worm has turned. States, starved for revenue, have upped the ante. See excerpts from a client alert from Day Pitney. 
"Business entities doing business in Connecticut without registration with the Secretary of the State have become a prime target for enforcement by top state officials. Secretary of the State Denise Merrill and Attorney General George Jepsen issued a joint press release last week, stating that out-of-state business entities that failed to register paid more than $1.3 million in penalties in fiscal year 2013. The largest penalty imposed was more than $54,000
Here is how Connecticut is more punitive than other states: Connecticut assesses a $300 penalty for each month, or $3,600 for each year, in which an out-of-state entity transacts business in the state without a certificate of authority (in addition to the overdue fees and accrued interest). The penalty increased to $300 per month from $165 per month in October 2009. There is no "cap" or maximum on this monthly penalty. For example, an LLC formed in another state that has conducted business in Connecticut without registration for three years would be obligated to pay the back fees plus interest plus a total of $10,800 in penalties. A large company headquartered in Connecticut with multiple subsidiaries organized elsewhere but "transacting business" in the state without registration could easily face penalties in the tens of thousands of dollars. "
The short of the matter is that companies should file in any State in which they "transact business" because the States either are or will be scouring the landscape for revenue and jobs, a la Connecticut. The definition of "transacting business" for this purpose is helpfully set out in the Day Pitney analysis:
Connecticut statutes do not define what types of activities constitute "transacting business." However, the statutes do give a nonexclusive list of activities that do not constitute "transacting business." For example, under the Connecticut Business Corporation Act, the following activities do not constitute "transacting business":
The question of whether or not other activities constitute "transacting business" is determined on a case-by-case basis. This has been litigated frequently in the courts, typically in the context of whether or not an unregistered company can bring a lawsuit.
 Swerdloff & Wiles, "Doing Business in CT: Failure to Register Proves Costly, "Day Pitney Alert, 7/23/2013.
Joseph W. Bartlett, Special Counsel, JBartlett@McCarter.com
Joseph W. Bartlett is special counsel in the Corporate, Securities and Financial Institutions practice. A recognized pioneer of the national private equity and venture capital bar, Mr. Bartlett contributed to the original models for private equity and fund of fund partnerships. His experience extends to alternative investments, venture capital, emerging companies, corporate restructurings, private equity and buyouts. Mr. Bartlett's practice includes serving as counsel to asset managers, including those of major public and private equity funds, with a focus on technology companies, and he has also served as trustee of a series of public mutual funds and chair of a public REIT. His venture fund work began with the first Greylock fund, and he has drafted documents for several of the largest and most successful LBO funds.
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Material in this work is for general educational purposes only, and should not be construed as legal advice or legal opinion on any specific facts or circumstances, and reflects personal views of the authors and not necessarily those of their firm or any of its clients. For legal advice, please consult your personal lawyer or other appropriate professional. Reproduced with permission from Joseph W. Bartlett. This work reflects the law at the time of writing in October 2013.