HILIC and RPLC chromatographies were used for an exhaustive metabolomic approach. A chemical database was created (n > 200) to identify affected urine metabolites. Urine metabolic profile is altered starting from 5 days following storage at +4C°. A number of urine metabolites profiles start being altered after a month at −20C°. −80 °C was considered as the most convenient urine long-term storage condition.