The aim of the present study is to describe the behavioral and emotional disturbances in the Fragile X Syndrome (FXS) and to analize the impact of having a member with FXS on different aspects of family functioning. A sample of 79 parents with a member with FXS and 80 parents with a member with typical development participated in the study. Results showed that between 17% and 66% of children and adolescents with FXS displayed significant behavioral and emotional disturbances and fewer prosocial behaviors. In addition, after controlling for behavioral and emotional difficulties, our results showed that families affected by FXS experienced a more negative impact on feelings about parenting, finances, siblings, and the degree of difficulty of living with a child or adolescent with FXS, and greater family adaptability and cohesion than the comparison group. In conclusion, our results highlight that it is important to consider these differences in clinical practice when supporting and counselling families affected by FXS.