Abstract Stuttering is a complex speech disorder and heritability of this trait is persuasive, with multiple afflicted families showing phenotypic segregation across generations, yet no conclusive genetic etiology could be identified. Analyzing multiplex families using exome sequencing(ES) may help in identification of putative genes and scope for understanding the mutational burden for speech implicated pathways. In this study ES was performed in six individuals from two clinically well characterized, multiple affected, south Indian families (STU-65 and STU-66) showing stuttering across five generations. From ES to variant prioritization, a sequential bioinformatics approach was implemented to search for putative gene targets. In the two multiplex families studied, ES data analysis resulted in an enriched list of 14 genes (with variants) (COL4A2,COL6A3,COL6A6,ITGAX,LAMA5,ADAMTS9,CSGALNACT1, TMOD2,HTR2B,RSC1A1,TRPV2,WNK1,ARSD and SPTBN5) involved in neural functions. Additionally, a homozygous variant in NLRP11 gene and a heterozygous variant in NAGPA gene were identified in STU-65 family that needs further confirmation. Our results support the fact that stuttering is a polygenic disorder. The putative gene targets identified in our study can drive the research prospects to understand the underlying mechanisms. We hypothesize multiple and combined mechanisms to be involved in the genesis of stuttering. Keywords: Stuttering, exome sequencing, neural pathways