Abstract Background It is debatable whether the size of triplet repeats of the fragile X mental retardation genes FMR1 and FMR2 (found at the FRAXA and FRAXE loci) is associated with Parkinson’s disease (PD). The aims of the current study were to investigate the relationship between these genes and PD and to determine whether these genes affected clinical manifestations of PD. Methods We recruited 206 PD patients and 227 control subjects from southern Spain. All subjects were screened for the size of CGG and CCG repeats at the FRAXA and FRAXE loci, respectively. Clinical features of each patient were examined in detail to study possible association between these features and genotype. Results Frequencies of FRAXA and FRAXE intermediate alleles were similar between PD and control groups. Clinical characteristics in PD patients, including severity of the disease, motor and non-motor symptoms, and motor complications and fluctuations were not affected by intermediate alleles at either locus. Two patients carrying FRAXA premutation alleles were identified showing clinical manifestations indistinguishable from idiopathic PD. Conclusions FRAXA and FRAXE intermediate alleles do not seem to affect the risk for PD or modify clinical features in PD patients.