Strain differences in perception, cognition and affect have been found to interact with the effect of experimental treatments on learning. The present study tested Dark Agouti (DA) and Wistar rats in conditioning to discrete and contextual stimuli, for strain differences in conditioned emotional response (CER) and effects of stimulus modality. A Pavlovian trace-conditioning procedure was used in which a discrete target stimulus (flashing light or tone, counterbalanced across groups) was paired either contiguously or at a 30-s trace with footshock. Contextual conditioning was assessed using a background (continuously presented) experimental stimulus (alternate to that used as target). Experiment 1 used 5 x 0.5 mA, 0.5-s footshock and Experiment 2 used 2 x 0.5 mA, 1-s footshock. In both experiments, conditioning to the discrete (target) and background stimuli interacted with strain of rat and stimulus modality. For conditioning to the target stimulus, the trace-conditioning effect (of relatively greater suppression in contiguously conditioned than trace-conditioned groups) differed by stimulus and strain. It was greater for the Wistar strain with the flashing light stimulus and for the DA strain with the click stimulus (although the latter was not significant in Experiment 1). In addition, suppression to the background stimulus was affected by stimulus modality for the DA but not Wistar strain in both experiments. DAs conditioned more to the click than the light as background, whereas there was no difference by stimulus modality for Wistars, although the exact pattern of how this stimulus modality effect was mediated differed between experiments. These results demonstrate that stimulus modality can be an issue when considering apparent strain differences in conditioning.