Abstract A comparative study has been performed for neutronic analysis of highly enriched in uranium (HEU) and potential low enriched in uranium (LEU) cores for the Pakistan Research Reactor-2 (PARR-2) taken as a typical miniature neutron source reactor (MNSR) system. The group constant generation has been carried out using transport theory code WIMS-D4 and a detailed five-group RZ-model has been used in the CITATION code for multigroup diffusion theory analysis. The neutronic analysis of the 90% HEU reference and potential LEU alternative: UO 2, U 3Si 2 and U9Mo, cores has been carried out yielding 11%, 20.7% and 14.25% enrichments with corresponding values of excess reactivity: 4.33, 4.30 and 4.07 mk. These results have been found in good agreement with recently reported Monte Carlo-based transport theory calculations. The diffusion theory-based calculated values of thermal flux profiles for axial as well as for radial directions have been found to agree well with the corresponding experimental measurements. The UO 2-based LEU core has been found having flux spectrum closest to the reference core while U9Mo core has significantly harder flux spectrum at irradiation site.