A study was conducted to determine the effect of including non-traditional ingredients on the flow and agglomeration properties of flour formulations, the rheological behavior of pasta dough, and the physical and cooked quality of the spaghetti. The effect of including non-traditional ingredients on the chemical changes that occurred in pasta during pasta making and cooking was also investigated. The formulations used were semolina 100% (S), whole wheat flour 100% (WW), semolina-whole wheat flour (49:51) (SWW), semolina-flaxseed flour (90:10), whole wheat flour-flaxseed flour (90:10), and semolina-whole wheat flour-flaxseed flour (39:51:10). Flaxseed flour was incorporated as fine (FF) or coarse (CF) particles. Depending on the experiment, formulations were hydrated to different levels that ranged between 10 and 34%. Study of the flow and agglomeration properties of the formulations indicated that samples containing whole wheat flour and or flaxseed flour were more cohesive and less prone to flow than samples with 100 or 90% semolina. Large agglomerate formation occurred with SFF hydrated beyond 30% moisture; whereas limited large agglomerate formation was detected in whole wheat samples with or without flaxseed flour hydrated up to 34% moisture. Rheological experiments showed that traditional and non-traditional pasta dough behaved like a shear thinning fluid that can be described by the Power Law model. Increased hydration levels and/or presence of flaxseed flour in the dough formulation decreased the apparent viscosity of the dough, which correlated with reduced extrusion pressure, mechanical energy, and specific mechanical energy required to extrude the dough. Better cooked quality was obtained for SWW than for WW, indicating that it is better to have some semolina in the formulation than replacing all the semolina with whole wheat flour. Inclusion of flaxseed flour gave better results when adding the flaxseed to 90% semolina than when adding it to WW or SWW. No chemical interaction was observed between the different ingredients during pasta making and/or cooking. Overall results indicated that the formulation-hydration combinations that optimized the processing and quality of non-traditional pasta products were: 30% for SFF, SCF, SWWFF, and SWWCF, 32% for S, WWFF, and WWCF, 33% for SWW, and 34% for WW.