The aim of this study was to examine the effect of chicken line on the contents of endogenous compounds, including carnosine, anserine, creatine, and inosine 5'-monophosphate (IMP), in breast and thigh meats from 5 lines of Korean native chicken for the development of high-quality meat breeds. Additionally, the effects of sex (male or female) and meat type (breast or thigh meat) were examined. In total, 595 F1 progeny [black: 90 (male: 45, female: 45); gray-brown: 110 (male: 52, female: 58); red-brown: 136 (male: 68, female: 68); white: 126 (male: 63, female: 63); and yellow-brown: 133 (male: 62, female: 71)] from 70 full-sib families were used. The male chicken from the red-brown line and the female chicken from the black line showed the highest BW among the 5 lines. Carnosine content was higher in female chicken and breast meat than in male chicken and thigh meat, respectively. Breast meat contained higher anserine content compared with thigh meat. The sex effect on anserine was not consistent between breast and thigh meat. Creatine content was not consistently influenced by sex between breast and thigh meat, and no meat type effect was observed. The IMP contents were higher in female chicken and breast meat compared with male chicken and thigh meat, respectively. In addition, we clearly observed line effects by the comparison of the contents of carnosine, anserine, creatine, and IMP for each meat type according to each sex. These data are useful for selection and development of high-quality, meat-type chicken breeds.