When foreign-born US residents apply for citizenship they painstakingly jump through every legal hoop, fill out endless forms, hand over wads of cash, and nervously await a response from the government for months and sometimes years.

They rightly expect their applications to be processed by the US Citizenship and Immigration Services (USCIS), which is a part of the Department of Homeland Security. They do not expect to have their citizenship application decided by a law enforcement agency like the Federal Bureau of Investigation (FBI).

But, for many Muslim applicants, we now know thanks to the ACLU, that the USCIS secretly consults the FBI to exercise a discretionary authority seemingly designed with Muslims in mind, to indefinitely postpone or deny applications if they deem the applicants “suspicious.”

The FBI does this through a secret program known obscurely as the Controlled Application Review and Resolution Program (CARRP). What’s shocking is that these immigrants who are either Muslim or perceived to be Muslim, never know why or for how long their applications are delayed. They are rarely, if ever, investigated for wrong-doing, and hence, have no opportunity to make their case for citizenship.

In 2009, I was an applicant for US citizenship who faced a similar mysterious delay.

After nine years of living in the US as a student, I married an American citizen and obtained my “Green Card” residency. Five years later I was finally eligible for citizenship. My application passed all the prescribed stages. Then, I undertook the second-to-last step – the dreaded citizenship exam – and passed with flying colors.

At this point I would normally have been handed a form telling me when and where to appear for the final step: my swearing-in ceremony. But the officer who administered the exam simply told me that the FBI was conducting a “background check” on me and that it could take a few days or a few months to complete. I was puzzled – I had already been fingerprinted and had no criminal record, nor had I ever broken any immigration laws.

So I waited. And waited. And waited.

USCIS is supposed to adjudicate applications within 6 months, but years went by. I wrote letters to no avail. In the mean time I refrained from traveling abroad to visit my family. I held back from covering protests as part of my journalism work for fear of being arrested and jeopardizing my citizenship application. I was unable to apply for residency for my younger sister who finished college and wanted to remain here. I couldn’t vote in the historic 2008 Presidential elections. My hardships were minor compared to what an undocumented immigrant faces. However, I fit the bill of the immigrant that “follows all the rules” and still, I was thwarted.

Finally, after contacting some immigrant advocacy organizations, I learned of a class-action lawsuit led by the ACLU and the National Immigration Law Center, representing people just like me – hundreds and thousands of people who had had their citizenship applications mysteriously and indefinitely delayed at the very last stage, most likely because of post-9-11 policies. I was not alone! Which was both a relief and a revelation of just how widespread the practice was.

I was named the lead plaintiff in the lawsuit and in 2009 the US government finally settled, forcing USCIS to hand me and hundreds of my fellow plaintiffs our citizenship. I dutifully waved an American flag, relieved that the process was finally over even though there was never any explanation given about the delay.

Although I am not Muslim, I am South Asian and was born and brought up in the United Arab Emirates, a Muslim Gulf Arab nation (and close US ally). I had traveled in 2005 to Afghanistan to research a book about the US war. I ran an organization that supported an Afghan women’s group critical of the war. I worked for a community radio network, Pacifica, known for being critical of the government. Perhaps it was some combination of these factors that led an FBI agent sitting at a desk somewhere to circle my name and put it on a pile of similar applications that would never get processed. I will never know.

And even though I and most others named in the lawsuit were given our citizenship, it turns out the FBI never really stopped delaying other applicants their citizenship. In fact, even among the class that I represented, there were some who were denied for no obvious reason.

Jennie Pasquarella is an ACLU attorney who worked on the class action lawsuit that I was part of and who authored a report on CARRP. She told me in an interview that although the US government settled our lawsuit in 2009 and was ordered to complete delayed applications like mine, the secret CARRP program had gone into effect a year earlier, in 2008, and it remained in effect, delaying applications for many other immigrants.

Pasquarella said this new FBI program is “effectively designed to identify people that they say are national security concerns. But of course the way they define national security concerns is heavily reliant on racial profiling, religious profiling, and is looking at people who are Muslim immigrants, members of our community.”

Pasquarella’s report on CARRP, just published by the ACLU, is based on declassified documents obtained through lawsuits and Freedom of Information Act Requests. The report profiles Muslims like Tarek Hamdi, an Egyptian, and Mahdi Asgari, an Iranian, who have had their applications delayed even though they have broken no laws.

The CARRP documents also reveal exactly how the USCIS transfers decision making over applications of people like Hamdi and Asgari to the FBI, asking the agency if they should be denied, approved, or simply delayed indefinitely. If the FBI decides that a certain application should be denied, the USCIS is authorized under CARRP, to search for a reason – even the most minor technical one such as reporting an erroneous date or address – to turn down an application when they ordinarily would not have.

The criteria for suspicion are predictably vague: people who are from or who travel to certain “suspicious” countries, who may be distantly affiliated with other “suspicious” people or institutions, people who have once upon a time given money to certain “suspicious” charities, and so on.

The US has a long history of discrimination in immigration, going back to the Chinese Exclusion Act of 1882. In 1952 the Immigration and Nationality Act was finally passed, prohibiting discriminatory immigration policies. Yet the FBI’s CARRP program, under the guise of post-9-11 suspicion of all persons Muslim being guilty of terrorism before they are proven innocent, does exactly that – it discriminates based on religion and nationality, and according to Pasquarella, returns to our immigration process “the discrimination that we long ago abolished.”

CARRP doesn’t just flag “suspicious” people in order to deny or delay their citizenship. The FBI has also used the program to dangle citizenship as a carrot for Muslims that it would like to turn into informants. The story of Hassan Razmara, an Iranian national, sordidly illustrates this: in February 2009 after years of waiting for his application to be processed, Razmara was approached by the FBI to become an informant in exchange for expediting his application. He could have agreed and after all, who would have blamed him?

Pasquarella says “[Razmara] had been attending a mosque [in Southern California] that the FBI had been surveilling so his application provided a great opportunity for them to say, ‘Hey Hassan, you know that citizenship application that … you’ve been waiting for a decision on for so long? We can make sure that you get a decision and that it’s favorable if you agree to work with us.’”

Hassan Razmara called the ACLU to find out if it was even legal for the FBI to do this. When Jennie Pasquarella told him it was absolutely not legal, he decided to follow his conscience and refused the FBI’s offer of being an informant in exchange for citizenship. As a result Hassan continues to wait year after year to become a US citizen.

It is not yet known how many people the CARRP program affects – not even those whose applications have been denied or delayed know for sure, because they are never informed of the reasons behind denial or delay – only the FBI and USCIS know. The ACLU has launched a lawsuit to force USCIS to reveal the numbers of people affected and it remains to be seen what will emerge.

Secret programs like CARRP give lie to the right wing rhetoric that undocumented immigrants simply need to get in line to legally obtain their papers just like everyone else. The problem is that, depending on where you come from, what your name sounds like, or what religion you are, the immigration system is set up to thwart you. And worst of all, you may not even realize it.