The leaf rust epidemic in 1978 shifted the focus of local wheat breeders to introduce new effective leaf rust genes from exotic sources (often obtained from CIMMYT and USDA) to the local varieties. However, the rapid changes in rust causing pathogen (Puccinia triticina) warrant deploying more efficient technologies for screening, selection and development of new varieties. Hence the present study was designed to focus on screening the presently available resistant genes in local wheat varieties, find the effective leaf rust resistance genes and to suggest a pre-breeding plan to combat future leaf rust incidence. Thirty-eight wheat varieties were selected some of which are still under cultivation especially in Punjab province and therefore hold importance in the commercial market. The data thus generated after field and molecular assisted screening were verified using sensitive ABI capillary electrophoresis (ABI 3730) to differentiate the closely located alleles as an efficient method to reduce the issues generated by conventional gel electrophoresis. The screening of leaf rust resistant genes revealed the presence of: Lr10, Lr13, Lr14a, Lr17, Lr26 and Lr27-Lr31 in 16, 16, 15, 16, 16 and 31 tested varieties respectively, while Lr34 also showed presence in 10 of the wheat varieties tested. The study reported absence of Lr9, Lr21 and Lr24 from the local germplasm making these genes as an appealing choice to introduce in local germplasm. Furthermore, screening of some newly mapped genes such as: Lr35, Lr46 and Lr47 showed complete absence while Lr39 was identified in 5 Pakistani varieties. The study was validated through the phenotypic data pertaining to these wheat germplasm grown under natural conditions at Regional Agriculture Research Centre, Bahawalpur (RARI) for three crop cycles (2009-10, 2010-11 and 2011-12). Hence, the assessed wheat varieties possessed more than one leaf rust resistant genes and showed a moderate level of resistance. The effective combinations under local conditions are: Lr14a, Lr17 and Lr26, while Lr34 has also been observed as efficient in combination with Lr10 and Lr27+Lr31. Following genes were found as the effective genetic combinations currently deployed in the field: Lr10, Lr13, L17, Lr27-31 and Lr34, Lr1, Lr10, Lr14a, Lr26, Lr27-31 and Lr34, Lr3, Lr10, Lr13, Lr14a, Lr17 and Lr27-31, Lr1, Lr26, Lr27-31 and Lr34, while several gaps have been identified where individual gene or gene combinations were not found in our varieties. These have been recommended for introduction in future pre-breeding programs.