Kleczynski and Harrison formally launched Malwarebytes on Januwhile Kleczynski was studying computer science at the University of Illinois.

RogueRemover proved instrumental in developing Malwarebytes Anti-Malware, and Kleczynski was able to set up a forum which enabled him to improve the software through feedback. In 2006, Kleczynski worked with a college roommate to produce a freely available program called 'RogueRemover', a utility which specialized in fighting against a type of infection known as 'rogues', which scam computer users into giving away their credit card information through fake anti-virus software. With one of the site's regulars, Bruce Harrison, Kleczynski wrote the inaugural version of the company's software. The company was unofficially founded after this, when Kleczynski conversed and became friends with several of the editors of the forum, who tempted him to buy an unused domain from them. It was only after Kleczynski posted on the forum SpywareInfo, popular at the time, that he was able to learn how to remove the virus, which took three days. He later recalled 'I've never been as angry as when I got my computer infected', and professed that his mother told him to fix it 'under penalty of death'. Kleczynski later discovered that, when his mother's computer became infected, neither McAfee nor Symantec would remove the malware from his system. He noticed that whenever infected computers arrived, the shop would typically reformat the computer entirely, rather than combat the virus, even if the infection was only minor.

CEO and founder Marcin Kleczynski, originally from Poland, was still a teenager attending high school in Bensenville, Illinois at the time, and was working as a technician in a computer repair shop in Chicago.

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