Clonazepam is a benzodiazepine drug having anxiolytic, anticonvulsant, muscle relaxant, sedative, and hypnotic properties. More common side effects with this medications are Drowsiness Interference with cognitive and motor performance Confusion Irritability and aggression Psychomotor agitation Lack of motivation Loss of libido Impaired motor function Impaired coordination Impaired balance Dizziness Cognitive impairments Hallucinations Short-term memory loss Anterograde amnesia (common with higher doses) As you can see menstrual disturbances are not the common side effect of this medication although it can happen as a rare side effect. Please consult a doctor if the problem persists. Take Care.