Coccidiosis, caused by different species of Eimeria, is an enteric disease in poultry that causes significant financial loss to the poultry industry. The objective of this research was to investigate the genetic components conferring resistance or susceptibility to a mixed Eimeria infection model in chickens. In this study, pedigreed offspring of White Leghorn chickens were used to evaluate the association of specific haplotypes of the major histocompatibility complex (MHC) B and alloantigen systems A (C4BPM), D (CD99), E (FCAMR), and I (RHCE) with the phenotypic traits being body weight gain (BWG), feed intake (FI), feed conversion ratio (FCR), gross and microscopic lesions, and oocyst shedding. The resistance traits such as higher BWG and reduced lesion severity were associated with the MHC B15, CD99-H01, RHCE-H01, and RHCE-H03 haplotypes. Further examination of these haplotype effects on coccidiosis resistance in commercial lines may validate their incorporation in selection programs.