The murdered journalists included Majid Charif, an editorialist with the monthly Iran é Farda , writer-journalists Mohamad Mokhtari and Mohammad Jafar Pouyandeh, and a couple, Darioush and Parvaneh Forouhar, who were freedom of expression activists.
He was initially charged with publishing information about the assassinations, imprisoned in December 2000, and was released after a month pending trial. In February 2002 he was tried in a military court behind closed doors with his lawyer present; the presiding judge was a prosecutor with the JOAF. While in detention, Zarafshan's office was reportedly searched, and weapons and alcohol were allegedly found.
He was sentenced on March 19, 2002 to five years' imprisonment (2 years for disseminating state secrets, 3 years for the possession of firearms) and 70 lashes for the possession of alcohol. Zarafshan denies the firearms and alcohol charges and claims these were planted in his office by the authorities.
Zarafshan was awarded the PEN/Barbara Goldsmith Freedom to Write Award in 2004.
Zarafshan has reportedly appealed to the Supreme Court and is currently awaiting a decision, which, according to information as of October 2002. During his imprisonment he was not only denied medical care for an urgent kidney disease for a period of time, but also was held in a cell with prisoners of violent crimes. On June 7, 2005 Zarafshan started a hunger strike to protest the absence of medical treatment. After a significant deterioration in his health, he ended his hunger strike and was hospitalized for an operation on his kidney in July 2005.
On March 16, 2007 after serving his sentence, Zarafshan was released from prison and told reporters, "I will now do the same things I did before."