The plant circadian clock primes the immune response of Arabidopsis thaliana to infection with the bacterial pathogen Pseudomonas syringae pv tomato DC3000 (Pst DC3000) such that there is a more robust response during the subjective day than subjective night. Thus Pst DC3000 growth in plants infected with the same initial titre of bacteria varies depending on the time of day of infection (Bhardwaj et al., PLoS One 6: e26968, 2011; Zhang et al., PLoS Pathog 9:e1003370, 2013). We describe here a protocol for assaying bacterial leaf titres following pressure infiltration or spray inoculation of Arabidopsis thaliana with Pst DC3000. We also describe a method for assaying plant susceptibility to infection with the necrotrophic fungal pathogen Botrytis cinerea. These methods can be used in studying the circadian clock regulation of signal transduction pathways controlling plant defense responses.