This paper deals with the work done on friction stir welding of thermoplastic material PA 6,6. A specially designed welding tool was used for this polymer. The major process parameters like tool rotational speed, feed rate were varied to understand the physical changes of the polymer and to carry out characterization studies. In this study, an attempt was made to optimize the process parameters by using L9 orthogonal array approach. ANOVA analysis was used to explore the effect of process parameters. Tensile testing was performed to analyze the joint strength. Thus, in new exploration of using polyamide 6,6 as base material, a maximum joint strength of 37 MPa has been achieved. Optimum combination of process parameters were found by using ANOVA studies. Microstructure of the friction stir welded joints using scanning electron microscopy was done. The X-ray diffraction and the thermogravimetric analysis were done to determine the degree of crystallinity and the level of degradation of the friction stir welded joints.