Three new salts of pefloxacin (PefH) with thiobarbituric (H2tba) and barbituric (H2ba) acids, pefloxacinium 2-thiobarbiturate trihydrate, PefH2(Htba)·3H2O (1), pefloxacinium 2-thiobarbiturate, PefH2(Htba) (2) and bis(pefloxacinium barbiturate) hydrate, (PefH2)2(Hba)2·2.56H2O (3) are synthesized and structurally characterized by the X-ray single-crystal diffraction. The structures of 1–3 contain intramolecular hydrogen bonds C–H⋯F, O–H⋯O. Intermolecular hydrogen bonds N–H⋯O and O–H⋯O form a 2D plane network in 1. In 2 and 3, intermolecular hydrogen bonds N–H⋯O form the infinite chains. In 1–3, the Htba− and Hba− ions are connected with PefH2 + only by one intermolecular hydrogen bond N–H⋯O. In 2 and 3, two Htba− and Hba− ions are connected by two hydrogen bonds N–H⋯O. These pairs form infinite chains. All three structures are stabilized by the π−π interactions of the head-to-tail type between PefH2 + ions. Compounds 2 and 3 are characterized by powder XRD, TG-DSC and FT-IR.