District sessions judge Vijay Laxmi yesterday rejected the plea of accused Niraj, Rampal and Upendra, citing there was no question of granting bail to them.
The three accused were arrested on charges of murder and rioting during communal violence at Bahawdi village in the district last year.
According to the prosecution, a person identified as Sagir was killed and and houses were burnt by the rioters in the village during the violence.
Police had registered a case against several people and arrested the three accused in connection with the incident.
The Special Investigation Team (SIT) probing the riots in the district had also found the trio involved in rioting and in killing of one person.
Muzaffarnagar and neighbouring districts including Shamli in western Uttar Pradesh had witnessed communal riots in September last year that left over 60 people dead and thousands of people displaced.