An ultra-centrifugal mill was evaluated by determining the effect of mill configuration and seed conditioning on particle size distribution and quality of whole-wheat (WW) flour. Ultra-centrifugal mill configured with rotor speed of 12,000 rpm, screen aperture of 250 μm, and seed conditioning moisture of 9% resulted in a fine WW flour where 82% of particles were <150 μm, starch damage was 5.9%, and flour temperature was below 35°C. The single-pass and multi-pass milling systems were evaluated by comparing the quality of WW flour and the subsequent WW spaghetti they produced. Two single-pass mill configurations for an ultra-centrifugal mill were used (fine grind: 15,000 rpm with 250 μm mill screen aperture and coarse grind: 12,000 rpm with 1,000 μm mill screen aperture) to direct grind durum grain or to regrind millstreams from roller milling to make WW flour and WW spaghetti. Particle size, starch damage, and pasting properties were similar for direct fine grind WW flour and multi-pass reconstituted flour:fine bran blend and for direct coarse grind WW flour and multi-pass reconstituted semolina:coarse bran blend. Semolna:fine bran or semolina:coarse bran blends made spaghetti with high cooked firmness, while spaghetti made from direct coarse grind or from semolina:fine bran or coarse bran blends had low cooking loss. Nineteen durum wheat (Triticum turgidum L. var. durum) cultivars and 17 breeding lines grown at 19 environments in North Dakota were evaluated for physical and cooking qualities of WW and traditional spaghetti. Of the 36 genotypes evaluated, 21 and 3 genotypes produced good and poor qualities of WW and traditional spaghettis, respectively, while other 12 genotypes produced good traditional spaghetti but produced poor quality WW spaghetti. These data indicate the need to select genotypes specifically for their WW pasta quality. Raw material traits (grain, semolina and WW flour characteristics) were evaluated to identify raw material traits capable of predicting WW spaghetti quality. Grain protein content had significant positive correlation with cooking quality of WW spaghetti. Stepwise multiple regressions showed grain protein content and mixogram break-time and wet gluten were the predominant characteristics in predicting cooking quality of WW spaghetti.