Limestone samples from Yandev and Odukpani limestone deposits in Nigeria were subjected to elemental analysis by Proton Induced X-ray Emission (PIXE) technique with the aim of broadening any database information on their elemental composition and concentration and accessing the extent of their environmental friendliness. The analysis was carried out with a 1.7 MV Tandem accelerator at the Center for Energy Research and Development (CERD), Ile Ife, Nigeria. In house calibration results involving the analysis of a NIST standard NBS 278 sample was used for quality assurance and control. Altogether fifteen different elements were observed in both locations. Fourteen elements that include Ca, Si, Al, Fe, K, Mg, Ti, S, Rb, P, Mn, Sr, Cl and Zn were observed in the Yandev deposit while ten elements including Ca, Si, Al, Fe, Na, Mg, K, Ti, Mn and Sr were observed in the Odukpani deposit. Some harmful rare earth elements (Ti, S, Rb, P, Mn, Cl, Sr and Zn) were observed only in the Yandev samples (except for Sr and Mn). These observations suggest that all particulate emissions and wastes from the Yandev deposit should be closely monitored to reduce its effects on the environment and health. The average Ca/Si ratio of the Yandev deposit is 4.32 while that of Odukpani deposit is 8.64. The observed low Ca/Si ratio in Yandev Limestone was attributed to the comparatively high Si content of the limestones. Thus the Odukpani limestone deposit appears to be more friendly to health and the environment.