In drug-facilitated crimes, victims are subjected to nonconsensual acts while they are incapacitated by the effects of a drug. A specific LC-MS/MS protocol for determining benzodiazepines and hypnotics at low concentration in hair specimens was developed and validated in order to target the allegedly administered drugs on a chronological basis. In the case hereby reported, a 26-year-old woman claimed to have been sexually assaulted after being administered an allegedly drugged coffee, but toxicological analysis of urine and blood provided no evidence of any drug intake. Subsequently, a second woman accused the same man of sexual abuse. Hence, the suspect was prosecuted. Specimens were collected from four subjects (two alleged victims, the suspect and his wife) and segmental hair analysis was performed. The results revealed that zolpidem was present at low picogram per milligram concentration in three out of eleven segments of hair specimen obtained from the first of the alleged victims, offering plain evidence of single or sporadic exposure, whereas the agent was detected in the high picogram per milligram range in the hair collected from suspect's wife, coherently with therapeutic administration. The presence of interfering signals typical of the keratin-containing matrix was found and possible hair degradation by cosmetic treatments was investigated by electron microscopy, so as to obtain a judicious interpretation of the analytical findings.