Barley yellow dwarf virus (BYDV) is a phloem-limited virus that is persistently transmitted by aphids and causes significant yield losses in wheat (Triticum aestivum L.). The present study was conducted to investigate the effects of BYDV in wheat on physiological and morphological traits, yield attributes and pasting properties of flour, and to determine any differences for these traits between susceptible and resistant genotypes under BYDV infection. Significant impact on physiological and morphological traits and yield was observed in plants inoculated at the 2-leaf stage (Zadoks scale, Z12), with a greater impact in the three susceptible genotypes than in the resistant genotype. Yield reduction with inoculation at Z12 was 18–49%, and yield reduction with inoculation mid tillering (Z25) was 6–31%. There was a significant reduction in effective tiller number with both inoculation times, but 1000-kernel weight was affected only with early inoculation. Pasting properties were little affected by BYDV infection, with genotype having a larger effect than infection. Grain yield showed negative correlation with tissue-blot immunoassay and visual symptom score, and positive correlation with all gas-exchange parameters, chlorophyll fluorescence, leaf area and biomass weight. The results suggest that stomatal conductance, transpiration rate and chlorophyll fluorescence measurements are suitable for assessment of BYDV infection and for screening BYDV of susceptible and resistant wheat genotypes.