Spot blotch caused by Cochliobolus sativus is a serious constraint to wheat (Triticum aestivum) yields in South Asia. A study was conducted at Rampur, Nepal, during 2002 and 2003 using five wheat genotypes (Sonalika, BL1473, Kanchan, Nepal 297 and NL 750) differing in spot blotch resistance to assess the effect of disease on loss of chlorophyll measured as soil plant analysis development (SPAD) over time characterised by the area under SPAD value decline curve (AUSDC) and the area under disease progress curve (AUDPC), and to investigate the association between disease severity and leaf anatomical traits. The SPAD value was measured using a Minolta SPAD-502 chlorophyll meter on three different dates in 10 randomly tagged flag leaves in each plot postanthesis to determine AUSDC. Eight anatomical characters were examined in the flag leaf. The AUDPC showed a significant negative correlation with the width of large vascular bundles, percentage of small vascular bundles with two girders and the number of large veins. The AUDPC was positively correlated with the distance between adjacent vascular bundles and leaf thickness. The SPAD and AUSDC values were higher in spot blotch resistant and tolerant genotypes. The findings underline the importance of mesophyll structure and chlorophyll content in spot blotch resistance in wheat. This is useful information for developing spot blotch resistant wheat.