Group A rotavirus (RVA) is the leading cause of diarrhea in children <5 years in many countries. The objectives of this pre-vaccination era study were to explore the prevalence and the genetic diversity of RVA strains in <5 years children, hospitalized due to gastroenteritis during 2014 – 2016. Two tertiary care hospitals Benazir Bhutto Hospital (BBH) located in Rawalpindi and Kharadar General Hospital (KGH) in Karachi were the study sites. A total of 1227 children were tested through ELISA for the presence of RVA and 28.5% (n=350) were found positive. From the 956 children enrolled in BBH (n=502 in 2014 and n=454 in 2015), 29.1% (n=279) were RVA positive. Among the 271 children enrolled in KGH during 2016, 26% (n=71) were found to be infected with RVA. A majority (78%; n=272) of RVA gastroenteritis cases were found in children <1 year of age and the virus was detected throughout the study period. Genotyping of ELISA positive samples through RT-PCR showed G12P[6] (21%) as the most dominant genotype followed by G3P[8] (16%), G2P[4] (12%), G1P[8] (9%), G9P[6] (8%) and G3P[6] (6%). A high proportion (10%) of mixed infection was also observed. Phylogenetic analysis clustered Pakistani G1 strains into two lineages, G1 lineage 1 & 2 along with strains from Russia, Australia, Thailand, India, Bhutan, Belgium Turkey, and the USA. The G2 strains clustered into G2 lineage IV, sub lineage IVa-3 along with strains reported worldwide. Pakistani G2 strains showed the D96N and S242N substitutions which are characteristic of sub-lineage IVa-3 and have been linked to the reemergence of these strains in many countries. Pakistan G3 viruses clustered into G3 lineage 3, sub-lineage 3d and were closely related to strains from China, Russia, Japan, and the USA. High amino acid similarities existed among indigenous G3 and the new variant G3 viruses that were first reported from Japan in 2003-2004. We hereby report the first finding of these variant G3 viruses from our country. The G9 strains grouped into two lineages G9 lineage 3 & 4 with the majority of strains belonging to lineage 3. Pakistani G12 strains belonged to the G12 lineage 3 together with G12 from different countries. The P[4], P[6] and P[8] Pakistani strains were linked to VP4 genotypes found globally. Comparative analysis of wild-type rotaviruses with RotarixTM and RotaTeqTM revealed several amino acid differences in the VP7 and VP8* antigenic epitopes. Notably, Pakistani G3 isolates contained a K238N amino acid change that generates an extra N linked glycosylation site which could have an effect on the antigenicity of these strains. This is the first report on the predominance of G12P[6] and the emergence of G3P[8] from Pakistan. Our findings provide important information pertinent to the genetic diversity of RVA strains circulating in the two cities of Pakistan (Rawalpindi and Karachi) and emphasize the need for large-scale epidemiological studies across the country.