Conventional method of species identification in Eimeria employs phenotypic characters of the oocysts and the site of infection in the chicken intestine, which are subjective analyses. PCR-based identification of Eimeria spp. is known to be specific and sensitive. We used internal transcribed spacer 1 (ITS-1)-based nested PCR to follow the distribution of Eimeria spp. in the field, which may be of significant value in the management of coccidiosis in chickens. In the present study, intestinal samples of chicks from commercial poultry farms, in India, suspected of having contracted Eimeria infections were analyzed using ITS-1 PCR. The PCR-amplified ITS-1 regions were also sequenced from these samples. Of 26 field samples analyzed, 19 showed the presence of multiple infections of Eimeria spp. Incidence of Eimeria tenella (80%) was found to be highest in these samples followed by Eimeria mitis (53%), Eimeria acervulina (42%), Eimeria brunetti, and Eimeria maxima (23%). Incidence of Eimeria necatrix was found to be the lowest (15%) in the samples analyzed, while none of the samples analyzed showed the presence of ITS-1 sequence from Eimeria praecox. The ITS-1 sequences amplified from Eimeria spp. in the present study showed few variations from the ITS sequences available in the GenBank database. Further studies will be required to determine whether these differences are unique to geographical locations.