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Simple Summary: Carps include some of the most widely farmed fresh water species. In the present study, the incidence of skeletal malformations in the fingerlings of four carp species reared in semi-intensive conditions in Albania was assessed. The investigated species were the common carp (Cyprinus carpio), silver carp (Hypophthalmichthys molitrix), grass carp (Ctenopharyngodon idella) and bighead carp (Hypophthalmichthys nobilis). The incidence of skeletal malformations and body growth were much higher in the herbivorous silver carp, grass carp and bighead carp than in the omnivorous common carp. We hypothesized that (i) the feeding protocol, which included ingredients of animal origin, may have caused an abnormal increase in the body growth rate associated with an increase in skeletal malformations in the herbivorous carp species; (ii) more efficient broodstock management may help increase egg quality and reduce skeletal malformations. Cyprinids include some of the most widely farmed freshwater species. The aim of this study was to assess the incidence of skeletal malformations in carp species reared in semi-intensive systems in Albania: common carp (Cyprinus carpio), silver carp (Hypophthalmichthys molitrix), grass carp (Ctenopharyngodon idella) and bighead carp (Hypophthalmichthys nobilis). The common carp fingerlings had a mean total length of 28.9 ± 5.0 mm; the frequencies of individuals with at least one anomaly and at least one severe anomaly were 79.2% and 43.4%, respectively. The silver carp juveniles had a mean total length of 21.6 ± 2.1 mm; the frequencies of individuals with at least one anomaly and one severe anomaly were 93.1% and 57.5%, respectively. The grass carp fry had a mean total length of 33.5 ± 2.6 mm; all the analyzed specimens showed almost one anomaly and 86.4% showed at least one severe anomaly. The bighead carp juveniles had a mean total length of 34.4 ± 5.7 mm; the frequencies of individuals with at least one anomaly and at least one severe anomaly were 95.0% and 62.5%, respectively. The development of a more suitable feeding protocol for herbivorous species and the setting up of more efficient broodstock management protocols are suggested to reduce the high incidence of skeletal malformations. [ABSTRACT FROM AUTHOR]